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Calcium in PDB 1iqc: Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea

Protein crystallography data

The structure of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea, PDB code: 1iqc was solved by H.Shimizu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.134, 55.111, 144.000, 90.00, 103.60, 90.00
R / Rfree (%) 22.2 / 25.7

Other elements in 1iqc:

The structure of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea (pdb code 1iqc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea, PDB code: 1iqc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 1iqc

Go back to Calcium Binding Sites List in 1iqc
Calcium binding site 1 out of 5 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca410

b:13.4
occ:1.00
 O A:THR239 2.4 10.9 1.0
O A:PRO241 2.4 13.9 1.0
O A:HOH1421 2.5 12.2 1.0
O A:HOH1426 2.5 10.9 1.0
OD1 A:ASN67 2.5 13.0 1.0
O A:HOH1425 2.5 11.3 1.0
O A:HOH1423 2.6 12.3 1.0
CG A:ASN67 3.5 12.5 1.0
C A:THR239 3.7 14.8 1.0
C A:PRO241 3.7 14.4 1.0
ND2 A:ASN67 3.9 14.8 1.0
O A:HOH1522 4.1 28.0 1.0
C A:TYR240 4.2 12.3 1.0
N A:PRO241 4.3 11.3 1.0
CA A:TYR242 4.3 13.6 1.0
CB A:THR239 4.3 9.9 1.0
O A:HOH1422 4.4 14.9 1.0
O A:ALA68 4.4 14.6 1.0
O A:HOH1458 4.5 13.6 1.0
OG1 A:THR239 4.5 12.2 1.0
N A:TYR242 4.5 14.5 1.0
O A:TYR240 4.5 14.2 1.0
O2A A:HEC402 4.5 17.3 1.0
N A:TYR240 4.5 11.7 1.0
CA A:TYR240 4.5 13.3 1.0
O1A A:HEC402 4.6 16.5 1.0
CA A:THR239 4.6 12.0 1.0
CA A:PRO241 4.7 16.9 1.0
CD2 A:TYR242 4.7 12.2 1.0
CB A:ASN67 4.8 12.3 1.0
O A:HOH1517 4.8 21.9 1.0
CGA A:HEC402 4.9 13.9 1.0
CD A:PRO241 4.9 12.5 1.0
O A:PHE243 5.0 17.8 1.0
C A:TYR242 5.0 13.5 1.0

Calcium binding site 2 out of 5 in 1iqc

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Calcium binding site 2 out of 5 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1411

b:30.7
occ:1.00
 OG1 A:THR257 2.9 21.5 1.0
O A:HOH1574 3.0 42.2 1.0
OE1 A:GLN253 3.1 34.8 1.0
O A:HOH1480 3.1 28.3 1.0
CG A:GLN253 3.6 26.9 1.0
CD A:GLN253 3.7 34.2 1.0
CB A:THR257 3.7 19.1 1.0
CE1 A:PHE243 3.8 13.2 1.0
CB A:ALA248 4.0 18.9 1.0
CG2 A:THR257 4.0 21.1 1.0
CE2 A:TYR206 4.0 24.1 1.0
O A:HOH1597 4.1 29.2 1.0
CD1 A:PHE243 4.2 15.3 1.0
O A:GLN253 4.4 18.9 1.0
OH A:TYR206 4.5 19.3 1.0
CA A:ALA248 4.6 17.3 1.0
O A:HOH1654 4.6 30.3 1.0
CZ A:TYR206 4.8 24.8 1.0
MG A:MG1420 4.8 32.3 1.0
O A:HOH1661 4.8 45.6 1.0
C A:GLN253 4.8 22.1 1.0
N A:ALA248 4.9 18.1 1.0
CB A:GLN253 4.9 24.4 1.0
CD2 A:TYR206 4.9 26.4 1.0
CZ A:PHE243 4.9 16.3 1.0

Calcium binding site 3 out of 5 in 1iqc

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Calcium binding site 3 out of 5 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca410

b:27.3
occ:1.00
 O B:PRO241 2.4 34.5 1.0
O B:HOH1414 2.6 23.0 1.0
O B:THR239 2.7 25.4 1.0
OD1 B:ASN67 2.7 23.6 1.0
O B:HOH1426 2.7 31.6 1.0
O B:HOH1456 2.7 29.4 1.0
O B:HOH1432 2.7 25.3 1.0
C B:PRO241 3.5 31.8 1.0
CG B:ASN67 3.5 27.2 1.0
ND2 B:ASN67 3.8 27.3 1.0
C B:THR239 3.9 25.5 1.0
CA B:TYR242 4.1 27.0 1.0
O B:HOH1502 4.2 29.2 1.0
N B:TYR242 4.2 27.7 1.0
N B:PRO241 4.2 20.9 1.0
C B:TYR240 4.3 23.6 1.0
O B:HOH1462 4.5 22.5 1.0
CA B:PRO241 4.5 26.7 1.0
O B:HOH1436 4.5 25.6 1.0
O B:ALA68 4.5 23.2 1.0
O1A B:HEC402 4.5 27.7 1.0
CB B:THR239 4.6 26.2 1.0
O2A B:HEC402 4.6 23.7 1.0
CA B:TYR240 4.6 23.2 1.0
O B:TYR240 4.7 28.4 1.0
CD2 B:TYR242 4.7 21.1 1.0
OG1 B:THR239 4.7 30.3 1.0
N B:TYR240 4.7 25.2 1.0
CD B:PRO241 4.8 24.4 1.0
CB B:ASN67 4.8 26.6 1.0
C B:TYR242 4.8 23.6 1.0
CA B:THR239 4.9 28.4 1.0
CG B:PRO241 4.9 23.7 1.0
CGA B:HEC402 4.9 22.0 1.0
O B:HOH1509 4.9 27.9 1.0
O B:PHE243 4.9 25.6 1.0
N B:PHE243 5.0 25.8 1.0

Calcium binding site 4 out of 5 in 1iqc

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Calcium binding site 4 out of 5 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca410

b:10.9
occ:1.00
 O C:PRO241 2.4 12.4 1.0
O C:THR239 2.4 12.2 1.0
O C:HOH411 2.4 12.3 1.0
OD1 C:ASN67 2.5 11.5 1.0
O C:HOH415 2.6 11.0 1.0
O C:HOH433 2.6 15.4 1.0
O C:HOH417 2.6 15.3 1.0
CG C:ASN67 3.5 19.2 1.0
C C:PRO241 3.6 13.8 1.0
C C:THR239 3.6 13.5 1.0
ND2 C:ASN67 3.9 11.9 1.0
O C:HOH458 4.0 24.5 1.0
C C:TYR240 4.2 11.7 1.0
N C:PRO241 4.2 12.6 1.0
CA C:TYR242 4.3 14.8 1.0
CB C:THR239 4.3 12.3 1.0
N C:TYR242 4.4 10.8 1.0
O C:HOH414 4.4 11.1 1.0
O C:ALA68 4.4 11.4 1.0
O C:TYR240 4.5 12.8 1.0
OG1 C:THR239 4.5 12.4 1.0
N C:TYR240 4.5 10.7 1.0
CA C:TYR240 4.5 12.0 1.0
O2A C:HEC402 4.5 14.1 1.0
O C:HOH436 4.5 16.7 1.0
CA C:THR239 4.6 10.8 1.0
CA C:PRO241 4.6 12.6 1.0
O1A C:HEC402 4.6 14.8 1.0
CD2 C:TYR242 4.6 12.1 1.0
O C:HOH441 4.8 20.4 1.0
CB C:ASN67 4.8 14.8 1.0
CD C:PRO241 4.8 15.6 1.0
CGA C:HEC402 5.0 16.1 1.0
C C:TYR242 5.0 15.7 1.0

Calcium binding site 5 out of 5 in 1iqc

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Calcium binding site 5 out of 5 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca410

b:29.8
occ:1.00
 O D:PRO241 2.4 27.4 1.0
O D:THR239 2.4 30.4 1.0
OD1 D:ASN67 2.5 29.9 1.0
O D:HOH2487 2.5 24.9 1.0
O D:HOH2486 2.6 24.4 1.0
O D:HOH2448 2.6 26.0 1.0
O D:HOH2485 2.7 37.4 1.0
CG D:ASN67 3.5 31.2 1.0
C D:PRO241 3.6 29.5 1.0
C D:THR239 3.7 23.7 1.0
ND2 D:ASN67 3.8 28.6 1.0
O D:HOH2509 3.9 42.8 1.0
C D:TYR240 4.2 25.0 1.0
O D:ALA68 4.3 27.6 1.0
N D:PRO241 4.3 23.2 1.0
CA D:TYR242 4.3 30.4 1.0
CB D:THR239 4.3 31.2 1.0
O D:HOH2427 4.4 35.9 1.0
O D:TYR240 4.4 27.2 1.0
N D:TYR242 4.5 28.2 1.0
CA D:TYR240 4.5 25.3 1.0
N D:TYR240 4.5 27.3 1.0
OG1 D:THR239 4.6 28.6 1.0
CA D:THR239 4.6 27.5 1.0
CA D:PRO241 4.6 24.7 1.0
O2A D:HEC402 4.7 35.2 1.0
O1A D:HEC402 4.7 28.2 1.0
CD2 D:TYR242 4.7 27.9 1.0
CB D:ASN67 4.7 31.0 1.0
CD D:PRO241 4.8 23.1 1.0
C D:TYR242 5.0 31.8 1.0

Reference:

H.Shimizu, D.J.Schuller, W.N.Lanzilotta, M.Sundaramoorthy, D.M.Arciero, A.B.Hooper, T.L.Poulos. Crystal Structure of Nitrosomonas Europaea Cytochrome C Peroxidase and the Structural Basis For Ligand Switching in Bacterial Di-Heme Peroxidases Biochemistry V. 40 13483 2001.
ISSN: ISSN 0006-2960
PubMed: 11695895
DOI: 10.1021/BI011481H
Page generated: Mon Jul 7 15:51:55 2025

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