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Calcium in PDB 1v3w: Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3

Enzymatic activity of Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3

All present enzymatic activity of Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3:
4.2.1.1;

Protein crystallography data

The structure of Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3, PDB code: 1v3w was solved by J.Jeyakanthan, T.H.Tahirov, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group F 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 156.156, 156.156, 156.156, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 20.3

Other elements in 1v3w:

The structure of Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3 (pdb code 1v3w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3, PDB code: 1v3w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1v3w

Go back to Calcium Binding Sites List in 1v3w
Calcium binding site 1 out of 4 in the Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3002

b:9.4
occ:0.50
 OD1 A:ASN61 2.3 7.9 1.0
OG A:SER40 2.4 14.8 1.0
CB A:SER40 3.3 11.8 1.0
CG A:ASN61 3.5 6.4 1.0
O A:SER40 3.7 11.7 1.0
CA A:SER40 4.2 8.0 1.0
ND2 A:ASN61 4.4 7.1 1.0
C A:SER40 4.4 7.6 1.0
CB A:ASN61 4.4 3.1 1.0
CA A:ASN61 4.6 5.8 1.0

Calcium binding site 2 out of 4 in 1v3w

Go back to Calcium Binding Sites List in 1v3w
Calcium binding site 2 out of 4 in the Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3003

b:17.7
occ:1.00
 O A:HOH3010 2.3 16.2 1.0
O A:HOH3016 2.4 21.1 1.0
O A:HOH3012 2.4 17.8 1.0
O A:HOH3011 2.5 23.2 1.0
O A:HOH3013 2.5 22.6 1.0
O A:HOH3009 2.5 17.6 1.0
O A:HOH3100 4.2 28.2 1.0
OE2 A:GLU32 4.3 25.7 0.5
OE1 A:GLU32 4.3 8.0 0.5
O A:HOH3022 4.5 45.8 1.0
OE1 A:GLU33 4.5 16.3 1.0
O A:HOH3113 4.7 27.1 1.0
CD A:GLU32 4.8 19.2 0.5
NE2 A:HIS14 4.8 13.7 1.0
OE1 A:GLU32 4.9 12.2 0.5
CD2 A:HIS14 5.0 11.5 1.0

Calcium binding site 3 out of 4 in 1v3w

Go back to Calcium Binding Sites List in 1v3w
Calcium binding site 3 out of 4 in the Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3004

b:16.2
occ:0.50
 O A:HOH3014 2.5 36.6 1.0
O A:HOH3015 2.5 22.9 1.0
OE1 A:GLU164 2.5 22.2 1.0
OE2 A:GLU164 2.6 29.9 1.0
CD A:GLU164 2.8 17.7 1.0
NZ A:LYS168 4.1 20.4 1.0
CG A:GLU164 4.3 18.5 1.0
O A:HOH3114 4.7 19.1 1.0
CE A:LYS168 4.9 20.4 1.0
O A:HOH3148 4.9 32.5 1.0

Calcium binding site 4 out of 4 in 1v3w

Go back to Calcium Binding Sites List in 1v3w
Calcium binding site 4 out of 4 in the Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Ferripyochelin Binding Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3005

b:36.0
occ:0.50
 ND2 A:ASN83 3.1 5.8 1.0
CB A:ASN83 3.7 2.6 1.0
O A:ASN83 3.7 8.5 1.0
CG A:ASN83 3.9 3.0 1.0
CA A:ASN83 4.4 5.5 1.0
C A:ASN83 4.5 7.3 1.0
OG A:SER100 4.6 17.4 1.0
O A:HOH3063 4.8 12.1 1.0

Reference:

J.Jeyakanthan, S.Rangarajan, P.Mridula, S.P.Kanaujia, Y.Shiro, S.Kuramitsu, S.Yokoyama, K.Sekar. Observation of A Calcium-Binding Site in the Gamma-Class Carbonic Anhydrase From Pyrococcus Horikoshii. Acta Crystallogr.,Sect.D V. 64 1012 2008.
ISSN: ISSN 0907-4449
PubMed: 18931408
DOI: 10.1107/S0907444908024323
Page generated: Tue Jul 8 02:52:40 2025

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