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Calcium in PDB 1ayp: A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement

Enzymatic activity of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement

All present enzymatic activity of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement:
3.1.1.4;

Protein crystallography data

The structure of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement, PDB code: 1ayp was solved by B.-H.Oh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.57
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.510, 114.720, 64.430, 90.00, 120.13, 90.00
R / Rfree (%) 21.4 / n/a

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement (pdb code 1ayp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement, PDB code: 1ayp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 1ayp

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Calcium binding site 1 out of 12 in the A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:7.6
occ:1.00
 O' A:INB201 2.1 10.1 1.0
OD2 A:ASP48 2.2 9.0 1.0
O2P A:INB201 2.2 9.8 1.0
O A:GLY31 2.4 14.0 1.0
O A:HIS27 2.4 11.0 1.0
O A:GLY29 2.5 10.9 1.0
OD1 A:ASP48 2.6 11.1 1.0
CG A:ASP48 2.7 8.9 1.0
C' A:INB201 3.2 11.1 1.0
C A:GLY31 3.5 17.9 1.0
P A:INB201 3.6 13.0 1.0
C A:HIS27 3.7 8.2 1.0
C A:GLY29 3.7 9.8 1.0
N A:GLY31 3.9 13.5 1.0
N A:GLY29 4.0 7.2 1.0
N2' A:INB201 4.0 10.6 1.0
CA A:GLY31 4.1 16.5 1.0
CB A:ASP48 4.1 7.6 1.0
C2' A:INB201 4.2 10.0 1.0
CM' A:INB201 4.2 6.0 1.0
O3P A:INB201 4.2 12.3 1.0
C3' A:INB201 4.4 6.0 1.0
CA A:GLY29 4.5 7.0 1.0
O3' A:INB201 4.5 10.8 1.0
CA A:HIS27 4.5 10.1 1.0
C A:VAL30 4.5 11.4 1.0
N A:CYS28 4.6 7.2 1.0
CA A:CYS28 4.6 6.1 1.0
N A:GLY32 4.6 15.7 1.0
N A:VAL30 4.7 10.8 1.0
O1P A:INB201 4.7 8.7 1.0
CB A:HIS27 4.8 6.4 1.0
C A:CYS28 4.8 9.7 1.0
O A:CYS44 4.8 11.5 1.0
CA A:VAL30 4.9 10.5 1.0
CA A:GLY32 5.0 17.1 1.0
CA A:ASP48 5.0 11.2 1.0

Calcium binding site 2 out of 12 in 1ayp

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Calcium binding site 2 out of 12 in the A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:24.5
occ:1.00
 O A:PHE23 2.2 16.9 1.0
O A:TYR112 2.4 20.4 1.0
O A:GLY25 2.5 21.7 1.0
OD1 A:ASN114 2.5 28.7 1.0
C A:PHE23 3.2 14.6 1.0
O A:HOH303 3.3 6.0 1.0
O A:CYS28 3.5 14.9 1.0
C A:GLY25 3.6 19.6 1.0
C A:TYR112 3.7 20.5 1.0
CG A:ASN114 3.7 29.2 1.0
CA A:PHE23 3.8 14.6 1.0
CB A:PHE23 4.2 15.0 1.0
N A:GLY25 4.2 12.9 1.0
C A:TYR24 4.2 11.8 1.0
N A:TYR24 4.3 13.5 1.0
O A:TYR24 4.4 12.9 1.0
ND2 A:ASN114 4.5 29.1 1.0
CA A:GLY25 4.5 15.9 1.0
N A:ASN114 4.5 22.4 1.0
CA A:TYR112 4.6 17.8 1.0
N A:CYS26 4.7 19.6 1.0
N A:TYR112 4.7 17.6 1.0
N A:SER113 4.7 22.2 1.0
CA A:TYR24 4.7 13.9 1.0
CA A:CYS26 4.7 19.2 1.0
CB A:TYR112 4.8 19.6 1.0
O A:CYS26 4.8 22.0 1.0
C A:CYS28 4.8 9.7 1.0
CB A:ASN114 4.8 25.7 1.0
C A:CYS26 4.9 19.0 1.0
CA A:ASN114 5.0 22.6 1.0

Calcium binding site 3 out of 12 in 1ayp

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Calcium binding site 3 out of 12 in the A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:13.3
occ:1.00
 O B:GLY29 2.2 12.0 1.0
OD1 B:ASP48 2.3 6.0 1.0
OD2 B:ASP48 2.4 9.9 1.0
O2P B:INB202 2.5 9.3 1.0
O B:GLY31 2.5 17.4 1.0
O B:HIS27 2.6 9.5 1.0
O' B:INB202 2.7 6.1 1.0
CG B:ASP48 2.7 6.0 1.0
C B:GLY29 3.4 12.1 1.0
C' B:INB202 3.5 9.6 1.0
C B:GLY31 3.7 18.3 1.0
C B:HIS27 3.7 11.5 1.0
P B:INB202 3.8 11.0 1.0
O B:VAL30 3.9 22.8 1.0
C B:VAL30 3.9 17.1 1.0
N B:GLY31 4.0 14.0 1.0
N B:GLY29 4.0 14.2 1.0
N2' B:INB202 4.1 9.4 1.0
C2' B:INB202 4.1 9.9 1.0
CB B:ASP48 4.2 8.1 1.0
C3' B:INB202 4.3 8.1 1.0
CA B:GLY31 4.3 14.4 1.0
N B:VAL30 4.3 13.8 1.0
O3' B:INB202 4.4 11.8 1.0
CA B:GLY29 4.4 10.8 1.0
CA B:VAL30 4.4 16.4 1.0
CM' B:INB202 4.4 6.0 1.0
CA B:HIS27 4.5 9.2 1.0
CA B:CYS28 4.6 10.1 1.0
N B:CYS28 4.6 10.6 1.0
C B:CYS28 4.6 13.1 1.0
O3P B:INB202 4.7 10.7 1.0
N B:GLY32 4.8 19.2 1.0
O1P B:INB202 4.9 9.6 1.0
CB B:HIS27 4.9 9.6 1.0

Calcium binding site 4 out of 12 in 1ayp

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Calcium binding site 4 out of 12 in the A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:18.9
occ:1.00
 OD1 B:ASN114 2.4 23.1 1.0
O B:GLY25 2.5 15.8 1.0
O B:PHE23 2.5 11.9 1.0
O B:TYR112 2.6 20.8 1.0
O B:TYR24 3.3 17.1 1.0
O B:HOH305 3.5 6.4 1.0
C B:PHE23 3.5 11.3 1.0
C B:GLY25 3.5 17.1 1.0
CG B:ASN114 3.6 22.4 1.0
C B:TYR112 3.7 17.7 1.0
C B:TYR24 3.8 13.9 1.0
O B:CYS28 4.0 16.2 1.0
CA B:PHE23 4.2 14.6 1.0
N B:GLY25 4.3 15.0 1.0
ND2 B:ASN114 4.3 21.2 1.0
N B:ASN114 4.4 16.5 1.0
N B:TYR24 4.4 10.7 1.0
N B:CYS26 4.4 15.3 1.0
CA B:CYS26 4.4 16.0 1.0
CA B:GLY25 4.5 14.3 1.0
CA B:TYR112 4.5 17.5 1.0
N B:TYR112 4.6 18.3 1.0
CA B:TYR24 4.6 13.3 1.0
O B:CYS26 4.6 19.4 1.0
CB B:PHE23 4.7 15.6 1.0
N B:SER113 4.7 16.0 1.0
C B:CYS26 4.7 16.4 1.0
C B:SER113 4.7 14.3 1.0
CB B:TYR112 4.7 16.2 1.0
CB B:ASN114 4.7 23.5 1.0
CA B:SER113 4.7 14.9 1.0
CA B:ASN114 4.9 22.0 1.0
C B:TYR111 5.0 21.8 1.0

Calcium binding site 5 out of 12 in 1ayp

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Calcium binding site 5 out of 12 in the A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca305

b:18.7
occ:1.00
 O C:GLY31 2.2 12.9 1.0
O C:HIS27 2.3 8.4 1.0
O2P C:INB203 2.4 8.6 1.0
OD1 C:ASP48 2.4 10.4 1.0
O C:GLY29 2.5 7.7 1.0
OD2 C:ASP48 2.6 7.5 1.0
O' C:INB203 2.7 7.9 1.0
CG C:ASP48 2.9 9.4 1.0
C C:GLY31 3.4 17.9 1.0
C C:HIS27 3.5 8.3 1.0
C C:GLY29 3.6 9.2 1.0
O C:VAL30 3.6 29.1 1.0
C' C:INB203 3.6 9.5 1.0
P C:INB203 3.7 8.7 1.0
C C:VAL30 3.7 21.9 1.0
N C:GLY31 3.9 20.6 1.0
O3' C:INB203 4.0 10.9 1.0
N C:GLY29 4.0 9.7 1.0
C2' C:INB203 4.0 10.4 1.0
CA C:GLY31 4.0 19.6 1.0
C3' C:INB203 4.1 7.0 1.0
N2' C:INB203 4.2 9.8 1.0
CA C:HIS27 4.4 8.9 1.0
CA C:VAL30 4.4 19.1 1.0
CB C:ASP48 4.4 8.2 1.0
N C:VAL30 4.4 13.9 1.0
CA C:GLY29 4.4 10.8 1.0
N C:CYS28 4.4 8.7 1.0
C C:CYS28 4.5 6.7 1.0
N C:GLY32 4.5 17.6 1.0
CA C:CYS28 4.6 8.3 1.0
O1P C:INB203 4.6 15.1 1.0
CM' C:INB203 4.7 6.1 1.0
O3P C:INB203 4.8 12.2 1.0
CB C:HIS27 4.8 9.4 1.0
CA C:GLY32 4.9 18.5 1.0
O C:CYS44 5.0 9.2 1.0

Calcium binding site 6 out of 12 in 1ayp

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Calcium binding site 6 out of 12 in the A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca306

b:21.9
occ:1.00
 O C:GLY25 2.5 18.6 1.0
O C:PHE23 2.5 22.1 1.0
O C:TYR112 2.5 20.1 1.0
OD1 C:ASN114 2.6 18.4 1.0
C C:PHE23 3.5 16.8 1.0
C C:GLY25 3.5 16.5 1.0
O C:HOH307 3.7 6.0 1.0
C C:TYR112 3.7 16.9 1.0
CG C:ASN114 3.8 11.6 1.0
O C:TYR24 4.0 14.8 1.0
CA C:PHE23 4.1 14.9 1.0
C C:TYR24 4.1 12.8 1.0
CB C:PHE23 4.1 14.3 1.0
N C:GLY25 4.1 13.1 1.0
O C:CYS28 4.2 7.5 1.0
N C:ASN114 4.3 16.8 1.0
CA C:GLY25 4.4 15.8 1.0
N C:CYS26 4.4 16.2 1.0
N C:TYR24 4.5 15.0 1.0
CA C:CYS26 4.5 17.7 1.0
ND2 C:ASN114 4.6 12.7 1.0
CA C:TYR112 4.6 14.3 1.0
N C:SER113 4.7 14.8 1.0
N C:TYR112 4.7 15.2 1.0
C C:SER113 4.7 16.0 1.0
CA C:ASN114 4.8 17.2 1.0
CA C:TYR24 4.8 14.6 1.0
CB C:TYR112 4.8 9.3 1.0
CB C:ASN114 4.8 15.1 1.0
O C:TYR111 4.8 19.6 1.0
CA C:SER113 4.9 17.1 1.0
C C:CYS26 4.9 16.7 1.0
C C:TYR111 4.9 17.2 1.0

Calcium binding site 7 out of 12 in 1ayp

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Calcium binding site 7 out of 12 in the A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca307

b:10.7
occ:1.00
 O D:GLY29 2.2 10.4 1.0
OD1 D:ASP48 2.2 11.8 1.0
O2P D:INB204 2.3 11.9 1.0
O D:GLY31 2.4 15.8 1.0
OD2 D:ASP48 2.4 13.1 1.0
O' D:INB204 2.5 6.4 1.0
O D:HIS27 2.6 9.7 1.0
CG D:ASP48 2.6 14.5 1.0
C' D:INB204 3.4 6.1 1.0
C D:GLY29 3.4 9.6 1.0
C D:GLY31 3.6 18.1 1.0
C D:HIS27 3.8 9.6 1.0
P D:INB204 3.8 10.1 1.0
N D:GLY31 3.9 18.2 1.0
C D:VAL30 4.1 19.3 1.0
N D:GLY29 4.1 8.9 1.0
CB D:ASP48 4.1 13.8 1.0
N2' D:INB204 4.3 6.0 1.0
CM' D:INB204 4.3 6.1 1.0
C2' D:INB204 4.3 8.7 1.0
O D:VAL30 4.4 24.7 1.0
CA D:GLY31 4.4 16.8 1.0
N D:VAL30 4.4 11.1 1.0
CA D:GLY29 4.4 9.3 1.0
CA D:VAL30 4.4 15.4 1.0
CA D:HIS27 4.4 10.7 1.0
O D:CYS44 4.5 8.6 1.0
O3' D:INB204 4.5 11.0 1.0
C3' D:INB204 4.6 7.9 1.0
CB D:HIS27 4.7 10.8 1.0
N D:GLY32 4.7 18.8 1.0
O1P D:INB204 4.7 6.6 1.0
O3P D:INB204 4.7 12.2 1.0
N D:CYS28 4.7 6.9 1.0
CA D:CYS28 4.7 6.2 1.0
C D:CYS28 4.8 6.1 1.0
CA D:ASP48 5.0 17.1 1.0

Calcium binding site 8 out of 12 in 1ayp

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Calcium binding site 8 out of 12 in the A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca308

b:19.6
occ:1.00
 O D:TYR112 2.4 21.7 1.0
O D:GLY25 2.4 17.1 1.0
OD1 D:ASN114 2.5 22.5 1.0
O D:PHE23 2.5 16.4 1.0
O D:TYR24 2.8 19.0 1.0
O D:HOH309 2.9 6.2 1.0
C D:PHE23 3.4 12.6 1.0
C D:GLY25 3.5 19.1 1.0
C D:TYR24 3.6 15.7 1.0
C D:TYR112 3.6 19.6 1.0
CG D:ASN114 3.6 23.6 1.0
O D:CYS28 4.0 10.2 1.0
CA D:PHE23 4.1 11.3 1.0
N D:TYR24 4.2 14.4 1.0
N D:GLY25 4.2 16.4 1.0
CA D:TYR24 4.4 15.1 1.0
CA D:GLY25 4.4 16.8 1.0
CB D:ASN114 4.5 25.5 1.0
N D:CYS26 4.5 22.6 1.0
CA D:TYR112 4.5 16.4 1.0
N D:TYR112 4.6 16.1 1.0
N D:ASN114 4.6 23.1 1.0
ND2 D:ASN114 4.7 26.6 1.0
CB D:PHE23 4.7 12.2 1.0
N D:SER113 4.7 20.7 1.0
CA D:CYS26 4.7 23.8 1.0
O D:CYS26 4.7 24.0 1.0
CB D:TYR112 4.8 12.8 1.0
C D:TYR111 4.8 17.4 1.0
C D:CYS26 4.9 22.7 1.0
CA D:ASN114 5.0 23.7 1.0

Calcium binding site 9 out of 12 in 1ayp

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Calcium binding site 9 out of 12 in the A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca309

b:10.3
occ:1.00
 O E:GLY29 2.2 12.1 1.0
O E:GLY31 2.2 16.3 1.0
OD1 E:ASP48 2.2 8.6 1.0
O2P E:INB205 2.3 10.6 1.0
OD2 E:ASP48 2.4 9.6 1.0
O E:HIS27 2.5 9.4 1.0
O' E:INB205 2.5 8.4 1.0
CG E:ASP48 2.7 7.7 1.0
C E:GLY31 3.4 20.5 1.0
C E:GLY29 3.5 13.2 1.0
C' E:INB205 3.5 7.6 1.0
C E:HIS27 3.5 9.7 1.0
N E:GLY31 3.6 26.4 1.0
P E:INB205 3.7 10.4 1.0
C E:VAL30 4.0 24.2 1.0
CA E:GLY31 4.0 22.6 1.0
N E:GLY29 4.1 6.6 1.0
C2' E:INB205 4.1 10.5 1.0
C3' E:INB205 4.2 6.9 1.0
CB E:ASP48 4.2 9.3 1.0
N2' E:INB205 4.2 8.7 1.0
O3' E:INB205 4.2 12.1 1.0
CA E:HIS27 4.3 12.1 1.0
N E:VAL30 4.4 16.3 1.0
CA E:VAL30 4.4 20.4 1.0
O3P E:INB205 4.4 7.0 1.0
CA E:GLY29 4.4 11.3 1.0
N E:CYS28 4.4 6.0 1.0
O E:VAL30 4.4 28.3 1.0
CM' E:INB205 4.5 6.0 1.0
N E:GLY32 4.5 18.8 1.0
CA E:CYS28 4.5 7.2 1.0
C E:CYS28 4.5 6.0 1.0
O E:CYS44 4.8 16.9 1.0
O1P E:INB205 4.8 12.2 1.0
CA E:GLY32 4.8 21.2 1.0
CB E:HIS27 4.8 11.6 1.0

Calcium binding site 10 out of 12 in 1ayp

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Calcium binding site 10 out of 12 in the A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of A Probe Molecule Composed of Seventeen Percent of Total Diffracting Matter Gives Correct Solutions in Molecular Replacement within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca310

b:21.6
occ:1.00
 O E:TYR112 2.4 18.2 1.0
O E:PHE23 2.5 15.1 1.0
OD1 E:ASN114 2.5 18.4 1.0
O E:GLY25 2.5 14.4 1.0
C E:PHE23 3.4 13.2 1.0
C E:GLY25 3.6 14.3 1.0
CG E:ASN114 3.6 14.2 1.0
O E:HOH311 3.6 6.5 1.0
C E:TYR112 3.6 19.2 1.0
O E:TYR24 3.8 17.4 1.0
O E:CYS28 3.9 7.5 1.0
CA E:PHE23 3.9 14.1 1.0
CB E:PHE23 4.1 11.4 1.0
C E:TYR24 4.1 14.0 1.0
ND2 E:ASN114 4.3 8.6 1.0
N E:GLY25 4.3 14.8 1.0
N E:TYR24 4.4 13.5 1.0
N E:CYS26 4.4 14.1 1.0
N E:ASN114 4.5 20.2 1.0
CA E:GLY25 4.5 15.8 1.0
CA E:TYR112 4.6 16.0 1.0
CA E:CYS26 4.6 14.8 1.0
CB E:ASN114 4.6 16.7 1.0
CB E:TYR112 4.6 14.3 1.0
N E:TYR112 4.7 13.8 1.0
N E:SER113 4.7 19.9 1.0
CA E:TYR24 4.8 13.4 1.0
C E:CYS26 4.8 13.4 1.0
CA E:ASN114 4.8 21.8 1.0

Reference:

B.H.Oh, B.-H.Oh. N/A N/A.
ISSN: ISSN 0907-4449
PubMed: 15299314
DOI: 10.1107/S0907444994010024
Page generated: Mon Jul 7 13:31:55 2025

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