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Calcium in PDB 3m83: Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure)

Protein crystallography data

The structure of Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure), PDB code: 3m83 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) 48.97 / 2.12
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 103.797, 104.431, 221.644, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure) (pdb code 3m83). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure), PDB code: 3m83:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3m83

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Calcium binding site 1 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure)


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 Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:21.9
occ:1.00
 O A:HOH695 2.3 23.9 1.0
O A:HOH448 2.3 13.4 1.0
OE1 A:GLU45 2.3 22.2 1.0
OD2 A:ASP58 2.4 25.3 1.0
O A:HOH477 2.4 15.7 1.0
CD A:GLU45 3.4 30.1 1.0
CG A:ASP58 3.4 19.1 1.0
CB A:ASP58 3.8 15.6 1.0
OE2 A:GLU45 4.0 28.4 1.0
O A:HOH693 4.2 23.8 1.0
CB A:GLU45 4.3 18.4 1.0
O A:HOH458 4.4 14.4 1.0
CG A:GLU45 4.4 20.7 1.0
O A:HOH778 4.4 26.8 1.0
O A:HOH478 4.4 15.8 1.0
O A:HOH1013 4.5 31.8 1.0
OD1 A:ASP58 4.5 17.7 1.0
NZ A:LYS70 4.7 13.7 1.0

Calcium binding site 2 out of 8 in 3m83

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Calcium binding site 2 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure)


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 Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:60.3
occ:1.00
 OE1 A:GLU26 2.4 39.7 1.0
O A:LYS22 2.4 24.7 1.0
O A:HOH989 2.6 31.3 1.0
O A:HOH1292 2.7 40.5 1.0
O A:HOH1400 2.7 51.4 1.0
OE2 A:GLU26 2.8 56.2 1.0
CD A:GLU26 2.9 47.8 1.0
O A:HOH576 3.0 20.1 1.0
C A:LYS22 3.6 23.4 1.0
CA A:ASP23 4.1 24.9 1.0
N A:ASP23 4.3 25.2 1.0
CG A:GLU26 4.4 34.8 1.0
CB A:ASP25 4.7 23.1 1.0
CA A:LYS22 4.7 26.4 1.0
O A:HOH677 4.7 23.5 1.0
C A:ASP23 4.7 22.4 1.0
OD2 A:ASP25 4.8 30.3 1.0
N A:ASP25 4.8 21.1 1.0
N A:PHE24 4.9 22.2 1.0
N A:GLU26 5.0 23.2 1.0

Calcium binding site 3 out of 8 in 3m83

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Calcium binding site 3 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure)


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 Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca408

b:62.1
occ:1.00
 OE1 B:GLU26 2.4 36.4 1.0
O B:HOH706 2.4 24.1 1.0
O B:LYS22 2.5 25.4 1.0
O B:HOH586 2.7 20.3 1.0
OE2 B:GLU26 3.0 56.5 1.0
CD B:GLU26 3.0 47.6 1.0
C B:LYS22 3.7 26.0 1.0
CA B:ASP23 4.4 24.6 1.0
O B:HOH482 4.4 16.0 1.0
CG B:GLU26 4.5 36.1 1.0
CB B:ASP25 4.5 22.7 1.0
OD2 B:ASP25 4.5 28.3 1.0
N B:ASP23 4.5 25.0 1.0
N B:ASP25 4.7 21.2 1.0
CA B:LYS22 4.7 29.4 1.0
C B:ASP23 4.8 22.6 1.0
N B:GLU26 4.9 22.7 1.0
N B:PHE24 4.9 22.2 1.0

Calcium binding site 4 out of 8 in 3m83

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Calcium binding site 4 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure)


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 Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:52.5
occ:1.00
 OE1 C:GLU26 2.2 38.1 1.0
O C:LYS22 2.4 25.1 0.5
O C:LYS22 2.5 24.9 0.5
O C:HOH499 2.6 17.1 1.0
O C:HOH885 2.7 29.1 1.0
O C:HOH1195 2.7 36.8 1.0
OE2 C:GLU26 2.8 56.4 1.0
CD C:GLU26 2.8 47.2 1.0
O C:HOH1248 2.9 38.7 1.0
C C:LYS22 3.6 25.2 0.5
C C:LYS22 3.6 25.6 0.5
O C:HOH1281 3.8 40.1 1.0
CA C:ASP23 4.2 24.9 1.0
CG C:GLU26 4.3 35.4 1.0
N C:ASP23 4.3 25.2 1.0
OD2 C:ASP25 4.4 33.2 1.0
O C:HOH698 4.5 23.9 1.0
CB C:ASP25 4.6 22.3 1.0
CA C:LYS22 4.7 26.9 0.5
C C:ASP23 4.7 22.4 1.0
N C:ASP25 4.7 21.2 1.0
CA C:LYS22 4.7 27.4 0.5
N C:PHE24 4.8 22.2 1.0
N C:GLU26 4.9 23.2 1.0

Calcium binding site 5 out of 8 in 3m83

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Calcium binding site 5 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure)


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 Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:22.8
occ:1.00
 O D:HOH712 2.3 24.4 1.0
OD2 D:ASP58 2.4 24.7 1.0
O D:HOH673 2.4 23.4 1.0
O D:HOH520 2.4 18.3 1.0
OE1 D:GLU45 2.5 27.4 1.0
CG D:ASP58 3.4 20.2 1.0
CD D:GLU45 3.4 30.6 1.0
CB D:ASP58 3.8 18.1 1.0
OE2 D:GLU45 4.0 25.1 1.0
O D:HOH996 4.1 31.4 1.0
O D:HOH556 4.3 19.5 1.0
CB D:GLU45 4.4 19.6 1.0
O D:HOH431 4.4 10.8 1.0
O D:HOH445 4.4 12.8 1.0
O D:HOH843 4.5 28.3 1.0
CG D:GLU45 4.5 19.9 1.0
OD1 D:ASP58 4.5 23.1 1.0
NZ D:LYS70 4.7 18.8 1.0

Calcium binding site 6 out of 8 in 3m83

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Calcium binding site 6 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure)


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 Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca405

b:58.8
occ:1.00
 O D:LYS22 2.6 32.0 1.0
OE1 D:GLU26 2.6 37.9 1.0
OE2 D:GLU26 2.8 56.7 1.0
O D:HOH582 2.9 20.2 1.0
CD D:GLU26 3.1 46.8 1.0
O D:HOH1330 3.1 42.5 1.0
C D:LYS22 3.6 28.6 1.0
CA D:ASP23 4.3 24.8 1.0
N D:ASP23 4.4 25.7 1.0
O D:HOH651 4.5 22.6 1.0
CG D:GLU26 4.6 36.3 1.0
CA D:LYS22 4.7 29.6 1.0
OD2 D:ASP25 4.7 34.5 1.0
C D:ASP23 4.9 22.5 1.0
CB D:ASP25 4.9 23.0 1.0
N D:PHE24 5.0 22.6 1.0

Calcium binding site 7 out of 8 in 3m83

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Calcium binding site 7 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure)


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 Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca407

b:58.0
occ:1.00
 OE2 E:GLU26 2.4 57.4 1.0
O E:LYS22 2.4 28.4 1.0
OE1 E:GLU26 2.5 38.7 1.0
O E:HOH1302 2.5 41.1 1.0
CD E:GLU26 2.8 48.1 1.0
O E:HOH711 2.8 24.3 1.0
C E:LYS22 3.5 27.0 1.0
CA E:ASP23 4.1 24.8 1.0
N E:ASP23 4.3 25.5 1.0
CG E:GLU26 4.3 36.1 1.0
O E:HOH932 4.3 30.1 1.0
C E:ASP23 4.6 22.5 1.0
CA E:LYS22 4.6 28.7 1.0
CB E:ASP25 4.7 23.2 1.0
N E:PHE24 4.8 22.8 1.0
OD2 E:ASP25 4.8 33.1 1.0
N E:ASP25 4.8 21.7 1.0
N E:GLU26 4.9 23.3 1.0

Calcium binding site 8 out of 8 in 3m83

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Calcium binding site 8 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure)


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 Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.12 A Resolution (Paraoxon Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca406

b:59.1
occ:1.00
 OE1 F:GLU26 2.3 38.7 1.0
O F:LYS22 2.4 31.1 1.0
O F:HOH741 2.6 25.3 1.0
O F:HOH1405 3.0 54.5 1.0
CD F:GLU26 3.0 46.9 1.0
OE2 F:GLU26 3.1 56.3 1.0
C F:LYS22 3.6 28.4 1.0
CA F:ASP23 4.2 24.9 1.0
N F:ASP23 4.4 25.4 1.0
O F:HOH719 4.4 24.8 1.0
OD2 F:ASP25 4.4 32.8 1.0
CG F:GLU26 4.5 36.4 1.0
CB F:ASP25 4.6 24.0 1.0
C F:ASP23 4.7 22.6 1.0
CA F:LYS22 4.7 31.3 1.0
N F:ASP25 4.7 21.7 1.0
N F:PHE24 4.8 22.6 1.0
N F:GLU26 4.9 23.6 1.0

Reference:

M.Levisson, G.W.Han, M.C.Deller, Q.Xu, P.Biely, S.Hendriks, L.F.Ten Eyck, C.Flensburg, P.Roversi, M.D.Miller, D.Mcmullan, F.Von Delft, A.Kreusch, A.M.Deacon, J.Van Der Oost, S.A.Lesley, M.A.Elsliger, S.W.Kengen, I.A.Wilson. Functional and Structural Characterization of A Thermostable Acetyl Esterase From Thermotoga Maritima. Proteins V. 80 1545 2012.
ISSN: ISSN 0887-3585
PubMed: 22411095
DOI: 10.1002/PROT.24041
Page generated: Sat Jul 13 13:28:57 2024

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