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Calcium in PDB 2q04: Crystal Structure of Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution

Protein crystallography data

The structure of Crystal Structure of Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution, PDB code: 2q04 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.34 / 2.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.870, 128.580, 108.430, 90.00, 108.43, 90.00
R / Rfree (%) 22.9 / 26

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution (pdb code 2q04). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution, PDB code: 2q04:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2q04

Go back to Calcium Binding Sites List in 2q04
Calcium binding site 1 out of 7 in the Crystal Structure of Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution


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 Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca211

b:48.6
occ:1.00
 O A:HOH232 2.4 30.1 1.0
O A:THR133 2.4 58.7 1.0
O A:GLY98 2.5 57.6 1.0
O A:HOH221 2.6 40.5 1.0
O A:HOH256 2.7 40.0 1.0
OG1 A:THR133 3.6 60.8 1.0
C A:THR133 3.6 57.6 1.0
C A:GLY98 3.7 59.0 1.0
N A:THR133 4.1 56.3 1.0
O A:LEU97 4.2 57.6 1.0
OG1 A:THR132 4.3 57.7 1.0
CA A:THR133 4.3 57.1 1.0
OE2 A:GLU134 4.4 61.8 1.0
OE2 A:GLU96 4.4 61.1 1.0
CA A:ALA99 4.5 59.4 1.0
CB A:THR133 4.5 58.0 1.0
N A:ALA99 4.5 60.3 1.0
NE2 A:HIS138 4.6 49.0 0.5
CA A:GLY98 4.6 58.5 1.0
O A:HOH239 4.7 46.2 1.0
N A:GLU134 4.7 58.0 1.0
CD A:GLU134 4.8 61.6 1.0
CE1 A:HIS138 4.8 50.5 0.5
CB A:ALA99 4.9 58.6 1.0
CA A:GLU134 4.9 56.8 1.0

Calcium binding site 2 out of 7 in 2q04

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Calcium binding site 2 out of 7 in the Crystal Structure of Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution


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 Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca212

b:68.7
occ:1.00
 OE1 B:GLU88 2.4 57.1 1.0
O A:GLY89 2.4 56.9 1.0
O A:SER87 2.5 54.8 1.0
CD B:GLU88 3.0 55.0 1.0
OE2 B:GLU88 3.1 54.7 1.0
O A:HOH255 3.1 57.2 1.0
C A:SER87 3.5 54.6 1.0
C A:GLY89 3.6 56.4 1.0
O A:GLU88 3.8 56.8 1.0
O B:HOH230 3.9 43.0 1.0
N A:ASN91 4.0 57.5 1.0
C A:GLU88 4.0 55.6 1.0
CA A:SER87 4.1 54.9 1.0
O A:HOH267 4.3 42.3 1.0
CG B:GLU88 4.3 55.0 1.0
CA A:ASN90 4.4 57.0 1.0
O A:ASN91 4.4 58.3 1.0
N A:GLY89 4.4 55.3 1.0
N A:ASN90 4.4 56.8 1.0
N A:GLU88 4.4 54.6 1.0
CA A:GLY89 4.6 55.7 1.0
CB A:SER87 4.6 54.8 1.0
CB B:GLU88 4.6 55.6 1.0
C A:ASN90 4.7 57.4 1.0
CA A:GLU88 4.7 55.1 1.0
C A:ASN91 4.8 57.3 1.0
CA B:GLU88 4.8 55.6 1.0
CA A:ASN91 4.9 57.3 1.0

Calcium binding site 3 out of 7 in 2q04

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Calcium binding site 3 out of 7 in the Crystal Structure of Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution


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 Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca211

b:48.1
occ:1.00
 O B:HOH255 2.3 48.3 1.0
O B:THR133 2.3 57.4 1.0
O B:GLY98 2.5 60.0 1.0
O B:HOH226 2.5 41.8 1.0
O B:HOH231 2.6 33.4 1.0
O B:HOH244 2.9 48.8 1.0
OG1 B:THR133 3.3 57.2 1.0
C B:THR133 3.5 56.0 1.0
C B:GLY98 3.6 59.0 1.0
N B:THR133 3.9 55.5 1.0
CA B:THR133 4.1 56.0 1.0
OE2 B:GLU134 4.3 63.1 1.0
O B:LEU97 4.3 57.5 1.0
OG1 B:THR132 4.3 58.4 1.0
CB B:THR133 4.3 56.3 1.0
OE2 B:GLU96 4.5 60.4 1.0
CA B:GLY98 4.5 58.5 1.0
NE2 B:HIS138 4.5 48.3 0.5
N B:ALA99 4.5 59.8 1.0
CA B:ALA99 4.6 59.4 1.0
N B:GLU134 4.6 56.1 1.0
CD B:GLU134 4.8 61.0 1.0
CA B:GLU134 4.9 56.0 1.0
CB B:ALA99 4.9 59.5 1.0
CE1 B:HIS138 4.9 49.7 0.5

Calcium binding site 4 out of 7 in 2q04

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Calcium binding site 4 out of 7 in the Crystal Structure of Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution


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 Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca211

b:73.2
occ:1.00
 O C:HOH223 2.4 60.8 1.0
O C:THR133 2.5 55.8 1.0
O C:GLY98 2.5 59.5 1.0
O C:HOH230 2.5 52.6 1.0
OG1 C:THR133 3.2 58.0 1.0
C C:THR133 3.6 56.5 1.0
C C:GLY98 3.7 59.1 1.0
N C:THR133 4.0 57.4 1.0
OE2 C:GLU134 4.2 61.4 1.0
CA C:THR133 4.2 56.9 1.0
CB C:THR133 4.3 57.4 1.0
O C:LEU97 4.3 56.9 1.0
OG1 C:THR132 4.3 58.3 1.0
CA C:GLY98 4.5 58.6 1.0
N C:ALA99 4.6 59.2 1.0
OE2 C:GLU96 4.6 62.1 1.0
CA C:ALA99 4.6 59.1 1.0
N C:GLU134 4.7 56.8 1.0
NE2 C:HIS138 4.8 60.7 1.0
CD C:GLU134 4.9 59.9 1.0
CA C:GLU134 5.0 56.5 1.0
CB C:ALA99 5.0 59.1 1.0

Calcium binding site 5 out of 7 in 2q04

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Calcium binding site 5 out of 7 in the Crystal Structure of Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution


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 Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca211

b:39.1
occ:1.00
 O D:HOH250 2.2 33.4 1.0
O D:HOH248 2.3 37.7 1.0
O D:HOH249 2.3 34.7 1.0
OG1 D:THR133 2.4 55.6 1.0
O D:THR133 2.5 56.6 1.0
O D:HOH222 2.7 30.2 1.0
C D:THR133 3.5 55.8 1.0
CB D:THR133 3.6 55.7 1.0
N D:THR133 3.9 56.2 1.0
CA D:THR133 3.9 56.2 1.0
OE2 D:GLU96 4.1 65.7 1.0
O D:GLY98 4.2 60.9 1.0
O D:HOH233 4.3 48.2 1.0
CE2 D:TYR135 4.3 54.2 1.0
O D:HOH226 4.5 38.4 1.0
N D:GLU134 4.7 56.3 1.0
CG2 D:THR133 4.7 56.9 1.0
OG1 D:THR132 4.7 57.3 1.0
O D:HOH230 4.7 37.1 1.0
CD2 D:TYR135 4.7 53.7 1.0
O D:LEU97 4.9 59.0 1.0

Calcium binding site 6 out of 7 in 2q04

Go back to Calcium Binding Sites List in 2q04
Calcium binding site 6 out of 7 in the Crystal Structure of Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution


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 Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca211

b:51.4
occ:1.00
 O E:ACY213 2.2 56.7 1.0
O E:THR133 2.5 58.2 1.0
OG1 E:THR133 2.7 56.7 1.0
C E:ACY213 2.9 57.8 1.0
OXT E:ACY213 3.0 58.5 1.0
C E:THR133 3.5 56.8 1.0
CB E:THR133 3.8 57.1 1.0
CA E:THR133 4.1 56.6 1.0
CE2 E:TYR135 4.1 55.2 1.0
N E:THR133 4.1 56.0 1.0
CH3 E:ACY213 4.3 56.0 1.0
O E:GLY98 4.4 61.0 1.0
CD2 E:TYR135 4.5 55.2 1.0
OE2 E:GLU96 4.6 62.6 1.0
N E:GLU134 4.7 56.7 1.0

Calcium binding site 7 out of 7 in 2q04

Go back to Calcium Binding Sites List in 2q04
Calcium binding site 7 out of 7 in the Crystal Structure of Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution


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 Acetoin Utilization Protein (ZP_00540088.1) From Exiguobacterium Sibiricum 255-15 at 2.33 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca211

b:68.5
occ:1.00
 O F:THR133 2.5 56.7 1.0
O F:GLY98 2.9 59.3 1.0
OG1 F:THR133 3.5 57.2 1.0
C F:THR133 3.7 56.4 1.0
C F:GLY98 4.0 58.8 1.0
N F:THR133 4.0 56.1 1.0
O F:LEU97 4.1 55.9 1.0
OG1 F:THR132 4.3 56.8 1.0
CA F:THR133 4.3 56.6 1.0
CB F:THR133 4.5 57.5 1.0
OE2 F:GLU134 4.6 62.5 1.0
OE2 F:GLU96 4.6 62.5 1.0
CA F:GLY98 4.7 58.2 1.0
N F:GLU134 4.8 56.5 1.0
NE2 F:HIS138 4.8 46.0 0.5
N F:ALA99 4.8 59.2 1.0
CA F:ALA99 4.9 59.4 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Tue Jul 8 07:49:57 2025

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