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Calcium in PDB 1i0x: Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal)

Enzymatic activity of Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal)

All present enzymatic activity of Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal):
3.1.27.3;

Protein crystallography data

The structure of Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal), PDB code: 1i0x was solved by J.De Swarte, S.De Vos, U.Langhorst, J.Steyaert, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.271, 59.696, 100.136, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal) (pdb code 1i0x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal), PDB code: 1i0x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 1i0x

Go back to Calcium Binding Sites List in 1i0x
Calcium binding site 1 out of 5 in the Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:20.3
occ:1.00
 O B:HOH729 2.5 17.6 1.0
O B:HOH724 2.5 17.9 1.0
O B:PHE50 2.5 19.9 1.0
C B:PHE50 3.6 19.1 1.0
N B:PHE50 4.0 19.6 1.0
CA B:PHE50 4.3 19.1 1.0
O B:HOH806 4.5 38.9 1.0
C B:ASP49 4.6 20.8 1.0
OH B:TYR56 4.6 14.6 1.0
N B:SER51 4.7 18.7 1.0
CB B:PHE50 4.7 17.8 1.0
O B:VAL52 4.9 15.3 1.0
CA B:SER51 5.0 19.2 1.0
CA B:ASP49 5.0 21.2 1.0

Calcium binding site 2 out of 5 in 1i0x

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Calcium binding site 2 out of 5 in the Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:33.3
occ:1.00
 O B:HOH746 2.4 38.2 1.0
O B:HOH842 2.5 42.9 1.0
O B:HOH839 2.5 39.2 1.0
O B:HOH721 2.6 30.2 1.0
O B:HOH748 2.7 25.4 1.0
O B:HOH782 2.8 39.6 1.0
ND2 B:ASN83 4.4 20.3 1.0
OH B:TYR24 5.0 14.1 1.0

Calcium binding site 3 out of 5 in 1i0x

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Calcium binding site 3 out of 5 in the Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:12.3
occ:1.00
 O C:HOH721 2.3 42.5 1.0
O C:HOH720 2.4 23.5 1.0
O C:HOH719 2.4 22.9 1.0
O C:SER64 4.2 25.0 1.0
OD1 C:ASP66 4.3 23.3 1.0
OD2 C:ASP66 4.5 22.3 1.0
O C:HOH773 4.7 25.2 1.0
O C:HOH795 4.8 40.3 1.0
CG C:ASP66 4.8 22.0 1.0
CB C:SER64 4.9 24.3 1.0

Calcium binding site 4 out of 5 in 1i0x

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Calcium binding site 4 out of 5 in the Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:14.2
occ:1.00
 O D:HOH832 2.4 22.9 1.0
O D:GLY47 2.4 9.1 1.0
O D:HOH721 2.5 22.7 1.0
O D:HOH705 2.6 21.2 1.0
OD1 D:ASP49 2.8 19.5 1.0
C D:GLY47 3.5 8.9 1.0
CG D:ASP49 3.9 20.3 1.0
CA D:GLY47 4.0 7.8 1.0
O D:HOH727 4.2 15.2 1.0
OD2 D:ASP49 4.4 24.9 1.0
N D:PHE48 4.6 9.9 1.0
N D:ASP49 4.8 13.2 1.0
C D:PHE48 4.8 11.5 1.0
O D:GLU46 4.8 9.5 1.0
CA D:PHE48 4.9 10.2 1.0
O D:HOH755 5.0 20.1 1.0

Calcium binding site 5 out of 5 in 1i0x

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Calcium binding site 5 out of 5 in the Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ribonuclease T1 in Complex with 2'Gmp (Form II Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca704

b:32.7
occ:1.00
 O D:HOH867 2.4 42.8 1.0
O D:ALA95 2.4 14.0 1.0
O D:HOH743 2.5 14.8 1.0
O D:HIS92 2.5 11.3 1.0
O D:HOH828 2.6 31.5 1.0
O D:HOH866 2.6 38.7 1.0
O D:HOH733 2.7 23.1 1.0
O D:HOH836 3.5 35.0 1.0
C D:HIS92 3.5 10.9 1.0
C D:ALA95 3.5 13.6 1.0
CB D:HIS92 3.8 9.6 1.0
O D:GLY97 4.1 13.9 1.0
CA D:HIS92 4.1 9.8 1.0
N D:ALA95 4.3 12.9 1.0
CA D:ALA95 4.3 12.8 1.0
O D:HOH745 4.4 20.9 1.0
N D:SER96 4.4 14.2 1.0
O D:HOH739 4.5 18.4 1.0
N D:THR93 4.5 9.6 1.0
CB D:ALA95 4.5 12.8 1.0
CA D:SER96 4.6 14.9 1.0
C D:SER96 4.7 14.5 1.0
CG D:HIS92 4.8 8.7 1.0
CA D:THR93 4.8 11.0 1.0
O D:SER96 4.8 14.0 1.0
O D:ASN99 4.9 11.8 1.0
N D:GLY94 4.9 12.3 1.0

Reference:

J.Deswarte, S.De Vos, U.Langhorst, J.Steyaert, R.Loris. The Contribution of Metal Ions to the Conformational Stability of Ribonuclease T1: Crystal Versus Solution. Eur.J.Biochem. V. 268 3993 2001.
ISSN: ISSN 0014-2956
PubMed: 11453993
DOI: 10.1046/J.1432-1327.2001.02310.X
Page generated: Thu Jul 11 10:13:36 2024

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