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Calcium in PDB 2e85: Crystal Structure of the Hydrogenase 3 Maturation Protease

Protein crystallography data

The structure of Crystal Structure of the Hydrogenase 3 Maturation Protease, PDB code: 2e85 was solved by T.Tanaka, T.S.Kumarevel, A.Shinkai, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.425, 54.984, 67.964, 90.00, 90.00, 90.00
R / Rfree (%) 24.8 / 25.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Hydrogenase 3 Maturation Protease (pdb code 2e85). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Hydrogenase 3 Maturation Protease, PDB code: 2e85:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2e85

Go back to Calcium Binding Sites List in 2e85
Calcium binding site 1 out of 6 in the Crystal Structure of the Hydrogenase 3 Maturation Protease


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 the Hydrogenase 3 Maturation Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:9.6
occ:1.00
 O A:ALA42 2.3 11.7 1.0
O A:GLY39 2.3 8.2 1.0
OD1 A:ASN45 2.3 13.2 1.0
O A:HOH1010 2.5 13.2 1.0
O A:HOH1018 2.5 13.2 1.0
OD1 A:ASP46 2.6 13.9 1.0
OD2 A:ASP46 2.6 14.7 1.0
CG A:ASP46 2.9 11.8 1.0
CG A:ASN45 3.4 14.2 1.0
C A:GLY39 3.4 9.2 1.0
C A:ALA42 3.5 12.2 1.0
ND2 A:ASN45 3.8 18.0 1.0
CA A:GLY39 3.9 8.3 1.0
N A:ALA42 4.2 13.8 1.0
CB A:ASP46 4.3 9.8 1.0
CA A:ALA42 4.3 13.1 1.0
N A:ASP46 4.4 9.9 1.0
N A:PRO43 4.4 12.0 1.0
CA A:PRO43 4.5 11.6 1.0
N A:GLY40 4.5 9.1 1.0
C A:ASN45 4.6 11.0 1.0
N A:ASN45 4.6 10.8 1.0
CB A:ASN45 4.6 11.6 1.0
O A:HOH1024 4.7 21.8 1.0
CA A:GLY40 4.7 10.2 1.0
C A:PRO43 4.7 11.4 1.0
C A:GLY40 4.8 11.0 1.0
CB A:ALA42 4.8 13.9 1.0
CA A:ASN45 4.8 11.6 1.0
CA A:ASP46 4.9 10.2 1.0
O A:HOH1029 4.9 22.6 1.0
O A:HOH1069 4.9 24.4 1.0
O A:HOH1073 4.9 19.0 1.0
N A:SER41 5.0 12.1 1.0

Calcium binding site 2 out of 6 in 2e85

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Calcium binding site 2 out of 6 in the Crystal Structure of the Hydrogenase 3 Maturation Protease


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 the Hydrogenase 3 Maturation Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:17.4
occ:1.00
 O A:HOH1062 2.2 22.8 1.0
O A:HOH1061 2.2 34.5 1.0
OD1 A:ASP116 2.2 10.1 1.0
O A:HOH1068 2.4 21.2 1.0
O A:HOH1015 2.4 15.4 1.0
O A:ASP116 2.5 11.4 1.0
O A:HOH1043 2.8 26.0 1.0
C A:ASP116 3.4 10.6 1.0
CG A:ASP116 3.5 9.6 1.0
CA A:ASP116 3.6 9.3 1.0
O A:HOH1126 4.0 35.0 1.0
CB A:ASP116 4.1 9.9 1.0
OD2 A:ASP116 4.5 10.2 1.0
O A:PRO115 4.5 8.2 1.0
N A:ILE117 4.6 8.7 1.0
O A:HOH1074 4.7 33.5 1.0
N A:ASP116 4.8 8.6 1.0

Calcium binding site 3 out of 6 in 2e85

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Calcium binding site 3 out of 6 in the Crystal Structure of the Hydrogenase 3 Maturation Protease


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 the Hydrogenase 3 Maturation Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:9.2
occ:1.00
 OD1 B:ASN45 2.2 12.2 1.0
O B:ALA42 2.3 12.3 1.0
O B:GLY39 2.3 10.6 1.0
O B:HOH1008 2.5 10.2 1.0
O B:HOH1010 2.5 10.0 1.0
OD2 B:ASP46 2.5 12.4 1.0
OD1 B:ASP46 2.6 12.6 1.0
CG B:ASP46 2.9 11.1 1.0
CG B:ASN45 3.3 13.3 1.0
C B:GLY39 3.4 10.1 1.0
C B:ALA42 3.5 11.8 1.0
ND2 B:ASN45 3.7 17.4 1.0
CA B:GLY39 4.0 10.7 1.0
N B:ALA42 4.2 12.7 1.0
CA B:ALA42 4.3 12.5 1.0
CB B:ASP46 4.3 10.3 1.0
N B:PRO43 4.4 11.4 1.0
N B:ASP46 4.5 9.2 1.0
CA B:PRO43 4.5 11.4 1.0
N B:GLY40 4.5 10.2 1.0
CB B:ASN45 4.6 11.1 1.0
C B:ASN45 4.6 10.4 1.0
O B:HOH1085 4.6 22.9 1.0
CB B:ALA42 4.6 12.8 1.0
N B:ASN45 4.7 9.2 1.0
C B:PRO43 4.7 11.0 1.0
C B:GLY40 4.8 10.4 1.0
CA B:GLY40 4.8 10.1 1.0
CA B:ASN45 4.9 10.5 1.0
CA B:ASP46 4.9 10.2 1.0
O B:HOH1021 4.9 20.3 1.0
O B:HOH1082 4.9 16.5 1.0
O B:PRO43 5.0 12.3 1.0
N B:SER41 5.0 11.6 1.0

Calcium binding site 4 out of 6 in 2e85

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Calcium binding site 4 out of 6 in the Crystal Structure of the Hydrogenase 3 Maturation Protease


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 the Hydrogenase 3 Maturation Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1004

b:19.6
occ:1.00
 O B:HOH1094 2.2 26.8 1.0
OD1 B:ASP62 2.3 18.5 1.0
OD1 B:ASP16 2.3 16.5 1.0
O B:HOH1047 2.4 36.1 1.0
O B:HOH1080 2.4 13.3 1.0
O B:ALA63 2.6 11.2 1.0
CG B:ASP62 3.2 14.2 1.0
CG B:ASP16 3.4 12.0 1.0
OD2 B:ASP62 3.4 24.9 1.0
O B:HOH1061 3.5 31.1 1.0
C B:ALA63 3.7 10.8 1.0
OD2 B:ASP16 3.8 16.8 1.0
N B:ALA63 4.0 9.5 1.0
CB B:ALA63 4.1 10.4 1.0
CA B:ALA63 4.2 9.1 1.0
O B:HOH1012 4.2 16.8 1.0
CA B:GLY9 4.6 8.8 1.0
CB B:ASP62 4.6 9.7 1.0
CB B:ASP16 4.7 9.7 1.0
C B:ASP62 4.7 9.0 1.0
O B:VAL8 4.7 8.1 1.0
O B:ASP16 4.8 9.0 1.0
CG1 B:VAL8 4.8 10.3 1.0
N B:THR64 4.9 10.8 1.0
CA B:ASP62 4.9 9.1 1.0
CA B:ASP16 5.0 9.1 1.0
O B:HOH1105 5.0 36.6 1.0

Calcium binding site 5 out of 6 in 2e85

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Calcium binding site 5 out of 6 in the Crystal Structure of the Hydrogenase 3 Maturation Protease


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 the Hydrogenase 3 Maturation Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1005

b:21.0
occ:1.00
 OD1 A:ASP99 2.3 21.2 1.0
OE1 B:GLN100 2.3 14.1 1.0
O B:HOH1079 2.3 49.4 1.0
OE1 B:GLU103 2.3 24.5 1.0
O A:HOH1063 2.4 36.6 1.0
O B:HOH1017 2.4 23.1 1.0
O B:HOH1051 2.5 27.9 1.0
CG A:ASP99 3.3 19.1 1.0
CD B:GLN100 3.3 16.0 1.0
CD B:GLU103 3.5 22.8 1.0
O B:HOH1128 3.6 59.8 1.0
NE2 B:GLN100 3.8 17.6 1.0
CB A:ASP99 3.9 13.6 1.0
CB B:GLU103 4.0 19.0 1.0
OD2 A:ASP99 4.4 23.4 1.0
CG B:GLU103 4.4 21.3 1.0
OE2 B:GLU103 4.4 25.6 1.0
OD1 B:ASP104 4.6 25.4 1.0
CG B:GLN100 4.6 13.9 1.0
O B:GLN100 4.7 11.9 1.0
CB B:GLN100 4.8 11.7 1.0
CA B:GLN100 4.8 11.3 1.0
O A:HOH1059 4.9 26.8 1.0

Calcium binding site 6 out of 6 in 2e85

Go back to Calcium Binding Sites List in 2e85
Calcium binding site 6 out of 6 in the Crystal Structure of the Hydrogenase 3 Maturation Protease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Hydrogenase 3 Maturation Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1006

b:21.9
occ:1.00
 O B:HOH1040 2.0 25.6 1.0
O B:HOH1072 2.3 29.0 1.0
O B:HOH1097 2.4 27.7 1.0
OE1 B:GLU140 2.4 22.4 1.0
O B:HOH1033 2.4 19.4 1.0
OE2 B:GLU140 2.7 22.0 1.0
O B:HOH1035 2.7 15.3 1.0
CD B:GLU140 2.9 22.1 1.0
CG B:GLU140 4.3 16.1 1.0
O B:HOH1078 4.4 25.1 1.0
NZ B:LYS31 4.5 18.0 1.0
O B:HOH1118 4.8 28.0 1.0

Reference:

T.Kumarevel, T.Tanaka, Y.Bessho, A.Shinkai, S.Yokoyama. Crystal Structure of Hydrogenase Maturating Endopeptidase Hyci From Escherichia Coli Biochem.Biophys.Res.Commun. V. 389 310 2009.
ISSN: ISSN 0006-291X
PubMed: 19720045
DOI: 10.1016/J.BBRC.2009.08.135
Page generated: Fri Jul 12 10:07:54 2024

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