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Calcium in PDB 3mq6: Domain Swapped Sgrai with Dna and Calcium Bound

Enzymatic activity of Domain Swapped Sgrai with Dna and Calcium Bound

All present enzymatic activity of Domain Swapped Sgrai with Dna and Calcium Bound:
3.1.21.4;

Protein crystallography data

The structure of Domain Swapped Sgrai with Dna and Calcium Bound, PDB code: 3mq6 was solved by P.W.Dunten, N.C.Horton, E.J.Little, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.46 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 130.384, 134.949, 237.485, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 26.1

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Calcium atom in the Domain Swapped Sgrai with Dna and Calcium Bound (pdb code 3mq6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 22 binding sites of Calcium where determined in the Domain Swapped Sgrai with Dna and Calcium Bound, PDB code: 3mq6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 22 in 3mq6

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Calcium binding site 1 out of 22 in the Domain Swapped Sgrai with Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Domain Swapped Sgrai with Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:31.3
occ:1.00
 OP1 K:DC8 2.3 29.6 1.0
OD2 A:ASP188 2.4 32.7 1.0
O A:HOH1179 2.5 25.7 1.0
O A:PHE241 2.5 29.2 1.0
O K:HOH1180 2.5 29.7 1.0
O A:HOH1178 2.6 30.7 1.0
OD1 A:ASP188 2.8 38.8 1.0
CG A:ASP188 3.0 33.3 1.0
P K:DC8 3.5 28.7 1.0
C A:PHE241 3.6 31.3 1.0
N A:PHE241 3.9 28.6 1.0
C5' K:DC8 3.9 29.8 1.0
O5' K:DC8 4.0 28.5 1.0
O K:HOH642 4.1 41.5 1.0
O K:HOH801 4.2 42.4 1.0
CA A:PHE241 4.2 28.4 1.0
OP2 K:DC8 4.3 36.1 1.0
O A:HOH343 4.4 24.0 1.0
CB A:ASP188 4.5 27.2 1.0
CB A:PHE241 4.5 25.0 1.0
O3' K:DA7 4.7 29.8 1.0
CG A:LYS242 4.7 35.5 1.0
N A:LYS242 4.7 31.6 1.0
OP2 K:DC9 4.7 30.0 1.0
O A:HOH368 4.7 34.7 1.0
C A:ALA240 4.9 30.9 1.0
CA A:LYS242 5.0 30.7 1.0
O A:HOH362 5.0 39.4 1.0

Calcium binding site 2 out of 22 in 3mq6

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Calcium binding site 2 out of 22 in the Domain Swapped Sgrai with Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Domain Swapped Sgrai with Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca340

b:45.3
occ:1.00
 OD1 A:ASN149 2.4 33.9 1.0
OE2 A:GLU103 2.5 46.9 1.0
O A:HOH1215 2.5 37.6 1.0
O A:LEU150 2.5 39.4 1.0
O A:HOH964 2.8 39.8 1.0
O A:HOH353 2.9 35.8 1.0
O A:HOH982 2.9 46.5 1.0
CD A:GLU103 3.2 46.8 1.0
OE1 A:GLU103 3.4 46.8 1.0
CG A:ASN149 3.4 36.8 1.0
C A:LEU150 3.5 34.3 1.0
ND2 A:ASN149 3.8 36.3 1.0
O A:ASP188 4.1 29.9 1.0
N A:LEU150 4.1 29.2 1.0
O K:HOH983 4.1 40.8 1.0
CA A:PRO151 4.2 37.0 1.0
N A:PRO151 4.3 35.7 1.0
C A:ASN149 4.4 35.5 1.0
O A:HOH358 4.4 37.2 1.0
CA A:LEU150 4.4 32.3 1.0
CG A:GLU103 4.6 34.0 1.0
O A:HOH980 4.7 40.0 1.0
C A:PRO151 4.7 40.5 1.0
CB A:ASN149 4.7 36.6 1.0
O A:ASN149 4.8 33.6 1.0
CA A:ASN149 4.9 35.2 1.0
N A:ARG152 5.0 35.7 1.0
C A:ASP188 5.0 33.6 1.0

Calcium binding site 3 out of 22 in 3mq6

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Calcium binding site 3 out of 22 in the Domain Swapped Sgrai with Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Domain Swapped Sgrai with Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca341

b:77.0
occ:1.00
 O A:SER153 2.6 39.7 1.0
O A:HOH1289 2.8 53.4 1.0
O A:HOH1288 2.9 58.7 1.0
OG A:SER153 2.9 44.3 1.0
C A:SER153 3.6 32.7 1.0
CB A:SER153 3.9 34.6 1.0
CA A:SER153 3.9 35.3 1.0
O A:HOH1118 4.2 45.7 1.0
N A:PHE154 4.8 33.1 1.0
O A:PHE154 4.8 32.7 1.0
O A:HOH355 4.9 31.2 1.0
C A:PHE154 5.0 37.7 1.0

Calcium binding site 4 out of 22 in 3mq6

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Calcium binding site 4 out of 22 in the Domain Swapped Sgrai with Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Domain Swapped Sgrai with Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca340

b:33.5
occ:1.00
 O B:HOH1176 2.4 31.0 1.0
O B:HOH1174 2.5 34.4 1.0
OD2 B:ASP188 2.5 32.7 1.0
OP1 L:DC8 2.5 31.9 1.0
O L:HOH1175 2.5 26.2 1.0
O B:PHE241 2.6 28.1 1.0
CG B:ASP188 3.2 37.6 1.0
OD1 B:ASP188 3.2 40.1 1.0
P L:DC8 3.5 34.9 1.0
C B:PHE241 3.7 35.5 1.0
O5' L:DC8 3.7 28.2 1.0
N B:PHE241 3.9 29.5 1.0
C5' L:DC8 4.0 31.9 1.0
OP2 L:DC8 4.2 31.0 1.0
O B:HOH365 4.2 38.7 1.0
CA B:PHE241 4.3 31.3 1.0
O B:HOH343 4.3 31.8 1.0
O B:HOH351 4.5 34.0 1.0
O B:HOH1128 4.5 43.6 1.0
CG B:LYS242 4.6 27.3 1.0
CB B:ASP188 4.6 31.4 1.0
OP2 L:DC9 4.6 28.1 1.0
CB B:PHE241 4.7 32.8 1.0
N B:LYS242 4.7 26.3 1.0
O3' L:DA7 4.8 37.3 1.0
C B:ALA240 4.8 32.6 1.0
CA B:LYS242 5.0 32.9 1.0

Calcium binding site 5 out of 22 in 3mq6

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Calcium binding site 5 out of 22 in the Domain Swapped Sgrai with Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Domain Swapped Sgrai with Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca341

b:48.9
occ:1.00
 OD1 B:ASN149 2.3 36.3 1.0
O B:LEU150 2.5 31.5 1.0
O B:HOH1226 2.6 41.5 1.0
OE2 B:GLU103 2.6 44.6 1.0
O B:HOH1224 2.7 34.5 1.0
O B:HOH1225 2.8 41.1 1.0
O B:HOH950 2.9 38.0 1.0
OE1 B:GLU103 3.2 44.3 1.0
CD B:GLU103 3.3 40.5 1.0
CG B:ASN149 3.3 32.1 1.0
ND2 B:ASN149 3.6 35.8 1.0
C B:LEU150 3.7 32.0 1.0
O B:HOH965 4.1 40.8 1.0
N B:LEU150 4.2 37.3 1.0
O B:ASP188 4.2 38.1 1.0
C B:ASN149 4.5 33.5 1.0
CA B:LEU150 4.5 29.9 1.0
N B:PRO151 4.6 33.2 1.0
CA B:PRO151 4.6 32.7 1.0
O B:HOH348 4.6 30.5 1.0
O B:HOH1128 4.7 43.6 1.0
CG B:GLU103 4.7 37.0 1.0
CB B:ASN149 4.7 35.0 1.0
OD1 B:ASP188 4.9 40.1 1.0
O B:HOH912 4.9 44.1 1.0
C B:PRO151 4.9 35.5 1.0
O B:ASN149 4.9 35.8 1.0
CA B:ASN149 5.0 30.4 1.0

Calcium binding site 6 out of 22 in 3mq6

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Calcium binding site 6 out of 22 in the Domain Swapped Sgrai with Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Domain Swapped Sgrai with Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca342

b:68.7
occ:1.00
 O B:SER153 2.6 35.5 1.0
O B:HOH1292 2.7 58.2 1.0
O L:HOH1293 3.0 51.6 1.0
O B:HOH1290 3.0 59.7 1.0
OG B:SER153 3.1 45.2 1.0
C B:SER153 3.6 41.5 1.0
CA B:SER153 3.9 33.4 1.0
CB B:SER153 3.9 36.4 1.0
O L:HOH271 4.6 37.4 1.0
N B:PHE154 4.8 34.9 1.0
O B:PHE154 4.9 31.4 1.0
C B:PHE154 5.0 37.7 1.0

Calcium binding site 7 out of 22 in 3mq6

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Calcium binding site 7 out of 22 in the Domain Swapped Sgrai with Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Domain Swapped Sgrai with Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca340

b:31.4
occ:1.00
 OP1 N:DC8 2.4 26.5 1.0
O C:HOH1170 2.4 32.3 1.0
OD2 C:ASP188 2.5 30.0 1.0
O C:PHE241 2.5 29.0 1.0
O C:HOH1172 2.5 30.0 1.0
O N:HOH1171 2.5 27.9 1.0
OD1 C:ASP188 3.0 36.5 1.0
CG C:ASP188 3.1 36.0 1.0
P N:DC8 3.6 31.3 1.0
C C:PHE241 3.6 25.7 1.0
N C:PHE241 3.8 34.6 1.0
O5' N:DC8 3.9 34.0 1.0
C5' N:DC8 4.0 34.6 1.0
CA C:PHE241 4.2 29.6 1.0
O N:HOH464 4.3 35.4 1.0
OP2 N:DC8 4.3 28.9 1.0
O N:HOH213 4.4 28.2 1.0
O C:HOH385 4.4 36.1 1.0
CG C:LYS242 4.5 35.4 1.0
CB C:ASP188 4.5 26.9 1.0
CB C:PHE241 4.6 26.6 1.0
OP2 N:DC9 4.6 27.7 1.0
O C:HOH354 4.7 32.0 1.0
N C:LYS242 4.7 29.8 1.0
O3' N:DA7 4.7 32.5 1.0
C C:ALA240 4.8 26.3 1.0
CA C:LYS242 5.0 31.7 1.0

Calcium binding site 8 out of 22 in 3mq6

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Calcium binding site 8 out of 22 in the Domain Swapped Sgrai with Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Domain Swapped Sgrai with Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca341

b:43.5
occ:1.00
 OD1 C:ASN149 2.3 35.2 1.0
O C:HOH1220 2.5 31.4 1.0
O C:LEU150 2.5 30.3 1.0
OE2 C:GLU103 2.6 42.9 1.0
O C:HOH914 2.7 37.7 1.0
O C:HOH746 2.8 40.0 1.0
O C:HOH352 2.8 40.1 1.0
CD C:GLU103 3.2 41.4 1.0
OE1 C:GLU103 3.2 48.0 1.0
CG C:ASN149 3.4 35.5 1.0
C C:LEU150 3.6 28.1 1.0
ND2 C:ASN149 3.8 35.0 1.0
O C:ASP188 4.1 31.9 1.0
N C:LEU150 4.2 29.9 1.0
CA C:PRO151 4.4 29.2 1.0
O C:HOH358 4.4 29.9 1.0
N C:PRO151 4.5 32.4 1.0
C C:ASN149 4.5 30.2 1.0
CA C:LEU150 4.5 34.5 1.0
CG C:GLU103 4.6 29.0 1.0
O C:HOH735 4.6 42.2 1.0
CB C:ASN149 4.7 30.9 1.0
C C:PRO151 4.8 32.3 1.0
N C:ARG152 4.9 28.2 1.0
CA C:ASN149 4.9 27.2 1.0
O C:ASN149 4.9 31.2 1.0

Calcium binding site 9 out of 22 in 3mq6

Go back to Calcium Binding Sites List in 3mq6
Calcium binding site 9 out of 22 in the Domain Swapped Sgrai with Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Domain Swapped Sgrai with Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca342

b:65.0
occ:1.00
 O N:HOH825 2.7 43.9 1.0
O C:SER153 2.7 35.5 1.0
O N:HOH791 2.7 43.6 1.0
OG C:SER153 3.0 45.2 1.0
C C:SER153 3.7 36.2 1.0
CB C:SER153 3.9 34.8 1.0
CA C:SER153 4.0 30.8 1.0
O N:HOH185 4.6 30.3 1.0
N C:PHE154 4.8 32.1 1.0
OP1 N:DC6 5.0 50.0 1.0

Calcium binding site 10 out of 22 in 3mq6

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Calcium binding site 10 out of 22 in the Domain Swapped Sgrai with Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Domain Swapped Sgrai with Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca340

b:29.5
occ:1.00
 OD2 D:ASP188 2.4 29.9 1.0
OP1 M:DC8 2.4 33.2 1.0
O D:HOH1188 2.4 27.7 1.0
O D:HOH1190 2.5 25.0 1.0
O M:HOH1189 2.5 25.3 1.0
O D:PHE241 2.5 32.1 1.0
OD1 D:ASP188 3.1 38.0 1.0
CG D:ASP188 3.1 32.0 1.0
P M:DC8 3.5 34.7 1.0
C D:PHE241 3.6 30.8 1.0
O5' M:DC8 3.9 28.3 1.0
N D:PHE241 3.9 29.2 1.0
C5' M:DC8 4.0 29.2 1.0
OP2 M:DC8 4.2 28.1 1.0
O D:HOH372 4.2 34.0 1.0
O M:HOH29 4.2 31.8 1.0
CA D:PHE241 4.2 30.4 1.0
O M:HOH675 4.2 39.2 1.0
O D:HOH423 4.4 33.8 1.0
CB D:ASP188 4.5 29.7 1.0
CB D:PHE241 4.6 24.2 1.0
OP2 M:DC9 4.6 31.0 1.0
CG D:LYS242 4.6 32.7 1.0
N D:LYS242 4.7 27.0 1.0
O3' M:DA7 4.8 30.3 1.0
C D:ALA240 4.8 32.5 1.0
O D:HOH629 4.8 37.4 1.0
CA D:LYS242 5.0 29.0 1.0

Reference:

C.K.Park, H.K.Joshi, A.Agrawal, M.I.Ghare, E.J.Little, P.W.Dunten, J.Bitinaite, N.C.Horton. Domain Swapping in Allosteric Modulation of Dna Specificity. Plos Biol. V. 8 E1000 2010.
ISSN: ISSN 1544-9173
PubMed: 21151881
DOI: 10.1371/JOURNAL.PBIO.1000554
Page generated: Sat Jul 13 13:43:01 2024

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