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Calcium in PDB 3m82: Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.40 A Resolution (Pmsf Inhibitor Complex Structure)

Protein crystallography data

The structure of Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.40 A Resolution (Pmsf Inhibitor Complex Structure), PDB code: 3m82 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 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 103.570, 104.500, 221.610, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 20.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.40 A Resolution (Pmsf Inhibitor Complex Structure) (pdb code 3m82). 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 2.40 A Resolution (Pmsf Inhibitor Complex Structure), PDB code: 3m82:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3m82

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Calcium binding site 1 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.40 A Resolution (Pmsf 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 2.40 A Resolution (Pmsf Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:21.2
occ:1.00
 O A:HOH448 2.3 12.8 1.0
O A:HOH477 2.4 8.0 1.0
OD2 A:ASP58 2.5 26.4 1.0
OE1 A:GLU45 2.5 25.6 1.0
CD A:GLU45 3.5 27.1 1.0
CG A:ASP58 3.5 20.1 1.0
CB A:ASP58 3.8 18.8 1.0
OE2 A:GLU45 4.0 20.2 1.0
O A:HOH778 4.3 27.9 1.0
CB A:GLU45 4.3 20.1 1.0
O A:HOH1013 4.3 28.7 1.0
O A:HOH458 4.4 12.6 1.0
O A:HOH693 4.4 14.9 1.0
CG A:GLU45 4.5 21.3 1.0
O A:HOH478 4.5 10.7 1.0
OD1 A:ASP58 4.6 24.0 1.0
NZ A:LYS70 4.6 16.9 1.0
O A:HOH709 4.9 28.0 1.0

Calcium binding site 2 out of 8 in 3m82

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Calcium binding site 2 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.40 A Resolution (Pmsf 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 2.40 A Resolution (Pmsf Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:64.7
occ:1.00
 OE1 A:GLU26 2.3 41.5 1.0
O A:LYS22 2.4 29.7 1.0
O A:HOH576 2.9 11.6 1.0
OE2 A:GLU26 2.9 59.1 1.0
CD A:GLU26 2.9 48.9 1.0
C A:LYS22 3.6 27.1 1.0
CA A:ASP23 4.2 22.9 1.0
N A:ASP23 4.4 24.4 1.0
CG A:GLU26 4.4 34.2 1.0
O A:HOH677 4.5 20.0 1.0
CB A:ASP25 4.5 22.8 1.0
N A:ASP25 4.6 23.5 1.0
C A:ASP23 4.7 22.8 1.0
OD2 A:ASP25 4.7 26.7 1.0
CA A:LYS22 4.7 31.0 1.0
N A:PHE24 4.8 22.7 1.0
N A:GLU26 4.8 24.1 1.0

Calcium binding site 3 out of 8 in 3m82

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Calcium binding site 3 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.40 A Resolution (Pmsf 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 2.40 A Resolution (Pmsf Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca408

b:64.4
occ:1.00
 O B:LYS22 2.6 29.5 1.0
O B:HOH586 2.6 21.9 1.0
OE2 B:GLU26 2.8 53.8 1.0
OE1 B:GLU26 2.9 46.3 1.0
CD B:GLU26 3.2 44.5 1.0
C B:LYS22 3.8 27.3 1.0
CA B:ASP23 4.5 22.6 1.0
O B:HOH482 4.6 20.5 1.0
CB B:ASP25 4.6 23.3 1.0
N B:ASP23 4.6 24.3 1.0
OD2 B:ASP25 4.7 25.2 1.0
CG B:GLU26 4.8 34.5 1.0
CA B:LYS22 4.8 31.3 1.0
N B:ASP25 4.9 23.6 1.0

Calcium binding site 4 out of 8 in 3m82

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Calcium binding site 4 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.40 A Resolution (Pmsf 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 2.40 A Resolution (Pmsf Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:60.4
occ:1.00
 O C:LYS22 2.4 30.1 1.0
OE1 C:GLU26 2.5 33.7 1.0
O C:HOH499 2.6 17.8 1.0
OE2 C:GLU26 2.6 42.6 1.0
O C:HOH1195 2.7 32.2 1.0
CD C:GLU26 2.9 41.4 1.0
O C:HOH885 3.1 22.2 1.0
O C:HOH1727 3.2 42.4 1.0
C C:LYS22 3.7 27.4 1.0
CA C:ASP23 4.3 22.6 1.0
OD2 C:ASP25 4.3 30.7 1.0
CG C:GLU26 4.4 35.8 1.0
N C:ASP23 4.4 24.0 1.0
O C:HOH698 4.4 22.3 1.0
O C:HOH1737 4.5 44.7 1.0
CA C:LYS22 4.7 31.4 1.0
CB C:ASP25 4.7 23.9 1.0
N C:ASP25 4.8 23.2 1.0
C C:ASP23 4.8 22.8 1.0
N C:PHE24 4.9 22.5 1.0

Calcium binding site 5 out of 8 in 3m82

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Calcium binding site 5 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.40 A Resolution (Pmsf 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 2.40 A Resolution (Pmsf Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:22.0
occ:1.00
 OE1 D:GLU45 2.4 23.6 1.0
O D:HOH673 2.4 14.5 1.0
OD2 D:ASP58 2.4 25.5 1.0
O D:HOH712 2.4 15.7 1.0
O D:HOH520 2.5 14.5 1.0
CD D:GLU45 3.3 26.8 1.0
CG D:ASP58 3.4 20.2 1.0
CB D:ASP58 3.8 17.3 1.0
OE2 D:GLU45 3.9 23.3 1.0
O D:HOH556 4.2 17.4 1.0
CB D:GLU45 4.3 19.1 1.0
O D:HOH445 4.4 9.8 1.0
CG D:GLU45 4.4 22.4 1.0
OD1 D:ASP58 4.5 26.0 1.0
NZ D:LYS70 4.7 17.9 1.0
O D:HOH843 4.8 33.3 1.0

Calcium binding site 6 out of 8 in 3m82

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Calcium binding site 6 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.40 A Resolution (Pmsf 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 2.40 A Resolution (Pmsf Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca405

b:65.5
occ:1.00
 OE1 D:GLU26 2.4 31.8 1.0
O D:LYS22 2.5 29.5 1.0
O D:HOH582 2.8 16.5 1.0
OE2 D:GLU26 2.9 48.8 1.0
CD D:GLU26 3.0 41.4 1.0
C D:LYS22 3.7 27.2 1.0
O D:HOH651 4.3 15.6 1.0
OD2 D:ASP25 4.4 30.4 1.0
CA D:ASP23 4.4 22.8 1.0
N D:ASP23 4.5 24.4 1.0
CG D:GLU26 4.5 35.2 1.0
CA D:LYS22 4.7 31.3 1.0
CB D:ASP25 4.7 24.0 1.0
N D:ASP25 4.9 23.7 1.0
C D:ASP23 4.9 23.0 1.0

Calcium binding site 7 out of 8 in 3m82

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Calcium binding site 7 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.40 A Resolution (Pmsf 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 2.40 A Resolution (Pmsf Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca407

b:65.7
occ:1.00
 OE1 E:GLU26 2.3 12.9 0.5
O E:LYS22 2.4 29.9 1.0
OE2 E:GLU26 2.8 33.1 0.5
CD E:GLU26 2.8 26.8 0.5
O E:HOH711 2.9 35.5 1.0
C E:LYS22 3.6 27.3 1.0
CA E:ASP23 4.1 22.7 1.0
CG E:GLU26 4.2 20.7 0.5
N E:ASP23 4.3 24.4 1.0
O E:HOH932 4.5 22.4 1.0
CB E:ASP25 4.6 25.2 1.0
C E:ASP23 4.6 23.1 1.0
N E:ASP25 4.6 23.7 1.0
OD2 E:ASP25 4.7 24.1 1.0
N E:PHE24 4.7 22.5 1.0
N E:GLU26 4.7 23.5 0.5
CA E:LYS22 4.8 31.3 1.0
N E:GLU26 4.8 21.8 0.5

Calcium binding site 8 out of 8 in 3m82

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Calcium binding site 8 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.40 A Resolution (Pmsf 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 2.40 A Resolution (Pmsf Inhibitor Complex Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca406

b:66.0
occ:1.00
 OE1 F:GLU26 2.2 17.0 0.5
O F:LYS22 2.6 29.7 1.0
O F:HOH741 2.7 16.9 1.0
CD F:GLU26 2.8 22.8 0.5
OE2 F:GLU26 2.9 27.2 0.5
C F:LYS22 3.8 27.4 1.0
CA F:ASP23 4.1 22.7 1.0
CB F:ASP25 4.2 25.8 1.0
CG F:GLU26 4.2 23.6 0.5
OD2 F:ASP25 4.3 25.4 1.0
N F:ASP23 4.4 24.1 1.0
N F:ASP25 4.4 23.8 1.0
N F:GLU26 4.5 24.1 0.5
N F:GLU26 4.5 22.7 0.5
O F:HOH719 4.5 25.1 1.0
C F:ASP23 4.6 23.1 1.0
N F:PHE24 4.7 22.8 1.0
CG F:ASP25 4.8 26.0 1.0
CA F:ASP25 4.8 23.4 1.0
CB F:GLU26 4.9 27.1 0.5
CA F:LYS22 5.0 31.4 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: Tue Jul 8 14:31:35 2025

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