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Calcium in PDB 2z0j: Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8

Protein crystallography data

The structure of Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8, PDB code: 2z0j was solved by N.Nakagawa, M.Kukimoto-Niino, S.Yokoyama, S.Kuramitsu, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.94 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.860, 65.004, 176.266, 90.00, 97.83, 90.00
R / Rfree (%) 18.8 / 21.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8 (pdb code 2z0j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8, PDB code: 2z0j:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2z0j

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Calcium binding site 1 out of 9 in the Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8


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 Uncharacterized Conserved Protein From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:4.3
occ:1.00
 O A:HOH483 2.4 23.4 1.0
O A:ILE25 2.4 6.0 1.0
O A:HOH473 2.5 14.0 1.0
OD1 A:ASP23 2.5 8.1 1.0
O A:HOH410 2.5 7.4 1.0
O A:HOH414 2.5 7.2 1.0
O A:HOH488 2.6 17.2 1.0
CG A:ASP23 3.4 7.9 1.0
C A:ILE25 3.4 7.0 1.0
OD2 A:ASP23 3.8 10.9 1.0
N A:ARG26 4.1 6.0 1.0
O A:HOH477 4.1 17.2 1.0
ND2 A:ASN98 4.2 16.5 1.0
O3S A:MES301 4.2 14.1 1.0
CB A:ALA196 4.4 7.0 1.0
N A:ILE25 4.4 5.9 1.0
O A:GLY142 4.4 8.3 1.0
CA A:ILE25 4.5 5.9 1.0
OD2 A:ASP151 4.5 7.7 1.0
OD2 A:ASP150 4.6 7.3 1.0
CB A:ASP23 4.6 7.3 1.0
OD1 A:ASP151 4.7 7.5 1.0
CB A:ILE25 4.7 5.9 1.0
CA A:ASP23 4.7 6.0 1.0
C A:ASP23 4.8 6.0 1.0
O2S A:MES301 4.9 14.6 1.0
CB A:ASN98 4.9 17.4 1.0
S A:MES301 4.9 18.7 1.0
O A:HOH461 4.9 18.3 1.0
C8 A:MES301 4.9 17.8 1.0
CG A:ASN98 4.9 17.9 1.0
CG A:ASP151 5.0 6.3 1.0

Calcium binding site 2 out of 9 in 2z0j

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Calcium binding site 2 out of 9 in the Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8


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 Uncharacterized Conserved Protein From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:9.6
occ:1.00
 O B:ILE25 2.4 11.7 1.0
O B:HOH437 2.5 16.0 1.0
OD1 B:ASP23 2.5 11.7 1.0
O B:HOH410 2.5 9.9 1.0
O B:HOH406 2.6 11.1 1.0
O B:HOH429 2.6 26.2 1.0
O B:HOH456 2.6 18.4 1.0
CG B:ASP23 3.4 11.1 1.0
C B:ILE25 3.4 10.4 1.0
OD2 B:ASP23 3.8 15.2 1.0
ND2 B:ASN98 4.0 31.4 1.0
N B:ARG26 4.1 9.6 1.0
O B:HOH426 4.2 14.9 1.0
O3S B:MES302 4.3 23.2 1.0
N B:ILE25 4.3 10.2 1.0
CA B:ILE25 4.4 9.3 1.0
CB B:ALA196 4.4 9.5 1.0
OD2 B:ASP151 4.5 10.5 1.0
O B:GLY142 4.5 10.3 1.0
OD2 B:ASP150 4.5 10.6 1.0
CB B:ASP23 4.6 9.6 1.0
OD1 B:ASP151 4.7 8.2 1.0
CA B:ASP23 4.7 8.6 1.0
O B:HOH493 4.7 30.6 1.0
CB B:ILE25 4.7 9.9 1.0
C B:ASP23 4.8 9.6 1.0
CB B:ASN98 4.8 30.9 1.0
CG B:ASN98 4.9 31.4 1.0
C8 B:MES302 5.0 22.1 1.0
S B:MES302 5.0 23.1 1.0

Calcium binding site 3 out of 9 in 2z0j

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Calcium binding site 3 out of 9 in the Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8


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 Uncharacterized Conserved Protein From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:8.3
occ:1.00
 O C:ILE25 2.4 9.3 1.0
OD1 C:ASP23 2.5 10.5 1.0
O C:HOH410 2.5 8.8 1.0
O C:HOH405 2.6 10.7 1.0
O C:HOH456 2.6 15.7 1.0
O C:HOH440 2.6 21.6 1.0
O C:HOH484 2.6 20.6 1.0
C C:ILE25 3.4 8.0 1.0
CG C:ASP23 3.4 10.9 1.0
OD2 C:ASP23 3.8 12.3 1.0
N C:ARG26 4.1 7.8 1.0
O C:HOH432 4.1 15.4 1.0
O3S C:MES303 4.2 23.1 1.0
ND2 C:ASN98 4.3 21.4 1.0
N C:ILE25 4.4 8.7 1.0
CA C:ILE25 4.4 7.8 1.0
CB C:ALA196 4.4 9.4 1.0
O C:GLY142 4.4 10.6 1.0
OD2 C:ASP151 4.5 9.8 1.0
OD2 C:ASP150 4.5 8.2 1.0
OD1 C:ASP151 4.6 9.3 1.0
CB C:ILE25 4.6 6.9 1.0
CB C:ASP23 4.6 8.6 1.0
CA C:ASP23 4.7 7.6 1.0
C C:ASP23 4.8 7.6 1.0
C8 C:MES303 4.9 23.6 1.0
O2S C:MES303 4.9 20.7 1.0
S C:MES303 5.0 25.7 1.0
CG C:ASP151 5.0 8.8 1.0

Calcium binding site 4 out of 9 in 2z0j

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Calcium binding site 4 out of 9 in the Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8


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 Uncharacterized Conserved Protein From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca404

b:10.2
occ:1.00
 O D:ILE25 2.4 10.2 1.0
O D:HOH415 2.5 11.3 1.0
O D:HOH447 2.5 16.0 1.0
OD1 D:ASP23 2.5 12.2 1.0
O D:HOH419 2.6 23.1 1.0
O D:HOH407 2.6 10.5 1.0
O D:HOH459 2.7 21.5 1.0
C D:ILE25 3.4 8.9 1.0
CG D:ASP23 3.4 11.0 1.0
OD2 D:ASP23 3.7 13.6 1.0
N D:ARG26 4.0 9.9 1.0
O D:HOH434 4.1 19.6 1.0
ND2 D:ASN98 4.2 20.4 1.0
O3S D:MES304 4.2 26.8 1.0
N D:ILE25 4.3 9.4 1.0
CB D:ALA196 4.3 10.0 1.0
CA D:ILE25 4.4 8.9 1.0
OD2 D:ASP151 4.5 11.1 1.0
OD2 D:ASP150 4.5 10.7 1.0
O D:GLY142 4.6 12.3 1.0
CB D:ASP23 4.6 9.3 1.0
OD1 D:ASP151 4.6 9.3 1.0
CB D:ILE25 4.7 9.3 1.0
CA D:ASP23 4.7 8.0 1.0
C D:ASP23 4.8 8.9 1.0
S D:MES304 4.9 28.9 1.0
CB D:ASN98 4.9 22.8 1.0
O2S D:MES304 4.9 25.0 1.0
CG D:ASP151 5.0 10.5 1.0
C8 D:MES304 5.0 27.1 1.0

Calcium binding site 5 out of 9 in 2z0j

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Calcium binding site 5 out of 9 in the Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8


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 Uncharacterized Conserved Protein From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:7.6
occ:1.00
 O E:ILE25 2.4 8.7 1.0
O E:HOH410 2.5 10.0 1.0
OD1 E:ASP23 2.5 12.1 1.0
O E:HOH453 2.5 15.9 1.0
O E:HOH407 2.6 11.0 1.0
O E:HOH441 2.6 18.3 1.0
O E:HOH452 2.6 14.2 1.0
C E:ILE25 3.4 9.1 1.0
CG E:ASP23 3.4 11.0 1.0
OD2 E:ASP23 3.8 13.5 1.0
O E:HOH425 4.1 15.0 1.0
N E:ARG26 4.1 10.3 1.0
O E:HOH462 4.3 22.0 1.0
N E:ILE25 4.3 8.4 1.0
CA E:ILE25 4.4 8.2 1.0
CB E:ALA196 4.4 10.7 1.0
OD2 E:ASP150 4.6 8.5 1.0
OD2 E:ASP151 4.6 9.8 1.0
CB E:ASP23 4.6 10.4 1.0
O E:GLY142 4.6 9.9 1.0
CA E:ASP23 4.7 9.4 1.0
OD1 E:ASP151 4.7 8.8 1.0
CB E:ILE25 4.7 9.3 1.0
OD1 E:ASN98 4.7 19.9 1.0
C E:ASP23 4.7 8.9 1.0
N E:VAL24 5.0 7.6 1.0

Calcium binding site 6 out of 9 in 2z0j

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Calcium binding site 6 out of 9 in the Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8


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 Uncharacterized Conserved Protein From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca406

b:8.1
occ:1.00
 O F:HOH414 2.5 10.3 1.0
OD1 F:ASP23 2.5 10.5 1.0
O F:ILE25 2.5 9.9 1.0
O F:HOH455 2.5 15.5 1.0
O F:HOH407 2.6 10.0 1.0
O F:HOH454 2.6 17.6 1.0
O F:HOH443 2.6 19.0 1.0
CG F:ASP23 3.4 11.3 1.0
C F:ILE25 3.5 8.8 1.0
OD2 F:ASP23 3.8 13.3 1.0
N F:ARG26 4.2 8.0 1.0
O F:HOH434 4.2 13.4 1.0
O F:HOH470 4.3 18.4 1.0
CB F:ALA196 4.4 11.6 1.0
N F:ILE25 4.4 7.8 1.0
CA F:ILE25 4.5 8.5 1.0
OD2 F:ASP150 4.6 7.9 1.0
OD2 F:ASP151 4.6 10.4 1.0
O F:GLY142 4.6 9.6 1.0
CB F:ASP23 4.6 9.0 1.0
CA F:ASP23 4.6 8.2 1.0
OD1 F:ASP151 4.6 8.4 1.0
O F:HOH523 4.7 29.2 1.0
CB F:ILE25 4.7 8.3 1.0
OD1 F:ASN98 4.8 24.3 1.0
C F:ASP23 4.8 7.3 1.0
N F:VAL24 5.0 7.3 1.0

Calcium binding site 7 out of 9 in 2z0j

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Calcium binding site 7 out of 9 in the Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca407

b:9.4
occ:1.00
 OD1 G:ASP23 2.5 12.6 1.0
O G:ILE25 2.5 11.6 1.0
O G:HOH443 2.5 15.6 1.0
O G:HOH414 2.5 13.2 1.0
O G:HOH410 2.5 9.9 1.0
O G:HOH454 2.6 20.4 1.0
O G:HOH489 2.6 25.8 1.0
CG G:ASP23 3.4 11.3 1.0
C G:ILE25 3.5 8.8 1.0
OD2 G:ASP23 3.7 15.6 1.0
N G:ARG26 4.1 9.8 1.0
O G:HOH427 4.1 14.5 1.0
O G:HOH438 4.3 25.0 1.0
N G:ILE25 4.4 8.2 1.0
CB G:ALA196 4.4 9.9 1.0
CA G:ILE25 4.5 9.1 1.0
O G:GLY142 4.5 12.0 1.0
OD2 G:ASP150 4.6 9.3 1.0
OD2 G:ASP151 4.6 10.1 1.0
CB G:ASP23 4.6 10.8 1.0
CA G:ASP23 4.7 9.4 1.0
OD1 G:ASP151 4.7 9.1 1.0
CB G:ILE25 4.7 9.4 1.0
C G:ASP23 4.8 9.8 1.0
OD1 G:ASN98 4.9 38.9 1.0
N G:VAL24 5.0 9.3 1.0
O G:HOH418 5.0 12.9 1.0

Calcium binding site 8 out of 9 in 2z0j

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Calcium binding site 8 out of 9 in the Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca408

b:10.5
occ:1.00
 OD1 H:ASP23 2.5 15.0 1.0
O H:HOH501 2.5 27.1 1.0
O H:ILE25 2.5 11.6 1.0
O H:HOH461 2.5 22.8 1.0
O H:HOH411 2.6 10.9 1.0
O H:HOH414 2.6 12.9 1.0
O H:HOH440 2.6 17.9 1.0
CG H:ASP23 3.3 15.7 1.0
C H:ILE25 3.4 9.6 1.0
OD2 H:ASP23 3.7 18.6 1.0
N H:ARG26 4.1 10.1 1.0
O H:HOH444 4.2 16.4 1.0
N H:ILE25 4.3 9.9 1.0
O H:HOH498 4.4 22.7 1.0
CB H:ALA196 4.4 11.7 1.0
CA H:ILE25 4.4 9.2 1.0
O H:GLY142 4.5 12.1 1.0
CB H:ASP23 4.6 12.5 1.0
OD2 H:ASP150 4.6 9.5 1.0
CA H:ASP23 4.6 11.3 1.0
OD2 H:ASP151 4.6 13.7 1.0
OD1 H:ASP151 4.7 10.4 1.0
C H:ASP23 4.7 9.9 1.0
CB H:ILE25 4.7 9.5 1.0
O H:HOH455 5.0 18.6 1.0
N H:VAL24 5.0 9.4 1.0

Calcium binding site 9 out of 9 in 2z0j

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Calcium binding site 9 out of 9 in the Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:11.5
occ:1.00
 OE1 A:GLU230 2.5 15.1 1.0
O A:HOH503 2.6 21.5 1.0
O F:HOH429 2.6 14.6 1.0
O F:HOH432 2.6 16.5 1.0
O A:HOH485 2.6 20.4 1.0
O F:HOH459 2.6 21.9 1.0
O F:GLY163 2.7 12.3 1.0
CD A:GLU230 3.4 15.1 1.0
OE2 A:GLU230 3.6 17.7 1.0
C F:GLY163 3.7 9.7 1.0
O F:HOH445 4.3 20.1 1.0
CA F:GLY163 4.4 9.3 1.0
N F:PHE164 4.6 9.0 1.0
CA F:PHE164 4.7 9.1 1.0
O F:GLY166 4.7 10.2 1.0
CG A:GLU230 4.7 13.0 1.0
C A:GLY229 4.7 7.8 1.0
N A:GLU230 4.7 8.5 1.0
O F:HOH411 4.8 9.7 1.0
CD1 F:PHE164 4.8 9.3 1.0
CB A:GLU230 5.0 9.8 1.0

Reference:

N.Nakagawa, M.Kukimoto-Niino, S.Yokoyama, S.Kuramitsu. Crystal Structure of Uncharacterized Conserved Protein From Thermus Thermophilus HB8 To Be Published.
Page generated: Fri Jul 12 19:37:11 2024

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