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Calcium in PDB 3m81: Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.50 A Resolution (Native Apo Structure)

Protein crystallography data

The structure of Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.50 A Resolution (Native Apo Structure), PDB code: 3m81 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) 48.80 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 103.460, 103.790, 221.020, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 21.2

Other elements in 3m81:

The structure of Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.50 A Resolution (Native Apo Structure) also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.50 A Resolution (Native Apo Structure) (pdb code 3m81). 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 2.50 A Resolution (Native Apo Structure), PDB code: 3m81:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3m81

Go back to Calcium Binding Sites List in 3m81
Calcium binding site 1 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.50 A Resolution (Native Apo 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 2.50 A Resolution (Native Apo Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:25.8
occ:1.00
 O A:HOH448 2.3 12.1 1.0
O A:HOH477 2.3 17.4 1.0
OE1 A:GLU45 2.4 36.2 1.0
OD2 A:ASP58 2.4 33.1 1.0
CD A:GLU45 3.4 34.6 1.0
CG A:ASP58 3.4 25.1 1.0
CB A:ASP58 3.9 25.3 1.0
OE2 A:GLU45 4.0 35.1 1.0
O A:HOH693 4.3 25.8 1.0
CB A:GLU45 4.3 27.9 1.0
O A:HOH458 4.3 21.1 1.0
OD1 A:ASP58 4.4 33.9 1.0
CG A:GLU45 4.4 31.8 1.0
O A:HOH478 4.5 17.3 1.0
NZ A:LYS70 4.6 26.0 1.0

Calcium binding site 2 out of 8 in 3m81

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Calcium binding site 2 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.50 A Resolution (Native Apo 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 2.50 A Resolution (Native Apo Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:69.7
occ:1.00
 OE2 A:GLU26 2.4 55.8 1.0
OE1 A:GLU26 2.5 50.8 1.0
O A:LYS22 2.6 34.1 1.0
CD A:GLU26 2.8 53.2 1.0
O A:HOH576 2.9 26.2 1.0
C A:LYS22 3.7 31.8 1.0
CG A:GLU26 4.3 37.8 1.0
CA A:ASP23 4.3 28.3 1.0
N A:ASP23 4.5 29.5 1.0
CB A:ASP25 4.6 26.4 1.0
O A:HOH677 4.7 32.5 1.0
OD2 A:ASP25 4.7 33.0 1.0
C A:ASP23 4.8 28.3 1.0
N A:ASP25 4.8 26.9 1.0
CA A:LYS22 4.8 34.8 1.0
N A:PHE24 4.9 27.8 1.0
N A:GLU26 5.0 30.0 1.0

Calcium binding site 3 out of 8 in 3m81

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Calcium binding site 3 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.50 A Resolution (Native Apo 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 2.50 A Resolution (Native Apo Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca408

b:64.8
occ:1.00
 O B:LYS22 2.3 33.7 1.0
O B:HOH1785 2.5 49.4 1.0
O B:HOH586 2.6 28.8 1.0
OE1 B:GLU26 2.6 52.3 1.0
OE2 B:GLU26 2.9 59.6 1.0
CD B:GLU26 3.1 48.5 1.0
C B:LYS22 3.6 31.8 1.0
O B:HOH482 4.2 18.2 1.0
CA B:ASP23 4.3 28.0 1.0
N B:ASP23 4.4 29.4 1.0
CA B:LYS22 4.6 35.1 1.0
OD2 B:ASP25 4.6 30.6 1.0
CG B:GLU26 4.7 32.6 1.0
CB B:ASP25 4.7 27.1 1.0
N B:ASP25 4.8 27.2 1.0
C B:ASP23 4.8 28.4 1.0
N B:PHE24 4.9 27.6 1.0

Calcium binding site 4 out of 8 in 3m81

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Calcium binding site 4 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.50 A Resolution (Native Apo 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 2.50 A Resolution (Native Apo Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:74.0
occ:1.00
 O C:HOH1195 2.2 32.1 1.0
OE1 C:GLU26 2.5 37.9 1.0
O C:LYS22 2.5 34.3 1.0
O C:HOH499 2.6 22.3 1.0
OE2 C:GLU26 2.9 51.4 1.0
CD C:GLU26 3.1 46.3 1.0
C C:LYS22 3.7 31.8 1.0
CA C:ASP23 4.5 28.4 1.0
OD2 C:ASP25 4.5 31.1 1.0
N C:ASP23 4.6 29.0 1.0
CG C:GLU26 4.7 38.1 1.0
CA C:LYS22 4.7 35.0 1.0
CB C:ASP25 4.9 25.9 1.0
N C:ASP25 5.0 27.1 1.0
C C:ASP23 5.0 28.1 1.0

Calcium binding site 5 out of 8 in 3m81

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Calcium binding site 5 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.50 A Resolution (Native Apo 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 2.50 A Resolution (Native Apo Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:30.3
occ:1.00
 OE1 D:GLU45 2.3 36.3 1.0
OD2 D:ASP58 2.3 33.2 1.0
O D:HOH520 2.4 28.4 1.0
CD D:GLU45 3.3 33.4 1.0
CG D:ASP58 3.3 22.6 1.0
OE2 D:GLU45 3.8 31.8 1.0
CB D:ASP58 3.8 24.5 1.0
OD1 D:ASP58 4.4 31.9 1.0
CB D:GLU45 4.4 26.1 1.0
O D:HOH445 4.4 16.9 1.0
CG D:GLU45 4.4 30.4 1.0
NZ D:LYS70 4.6 24.8 1.0

Calcium binding site 6 out of 8 in 3m81

Go back to Calcium Binding Sites List in 3m81
Calcium binding site 6 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.50 A Resolution (Native Apo 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 2.50 A Resolution (Native Apo Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca405

b:66.5
occ:1.00
 OE1 D:GLU26 2.2 19.9 0.5
O D:LYS22 2.6 34.0 1.0
O D:HOH582 2.7 21.6 1.0
OE2 D:GLU26 2.8 24.9 0.5
CD D:GLU26 2.8 22.9 0.5
O D:HOH1780 2.9 45.0 1.0
C D:LYS22 3.7 31.9 1.0
CA D:ASP23 4.2 28.5 1.0
CG D:GLU26 4.3 25.8 0.5
O D:HOH651 4.3 22.4 1.0
N D:ASP23 4.4 29.4 1.0
CB D:ASP25 4.5 27.1 1.0
N D:ASP25 4.6 27.5 1.0
C D:ASP23 4.6 28.4 1.0
N D:GLU26 4.7 28.7 0.5
N D:GLU26 4.7 30.1 0.5
N D:PHE24 4.7 27.7 1.0
CA D:LYS22 4.8 35.0 1.0
OD2 D:ASP25 4.9 35.0 1.0
CB D:GLU26 5.0 27.8 0.5

Calcium binding site 7 out of 8 in 3m81

Go back to Calcium Binding Sites List in 3m81
Calcium binding site 7 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.50 A Resolution (Native Apo 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 2.50 A Resolution (Native Apo Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca407

b:65.8
occ:1.00
 O E:LYS22 2.3 34.5 1.0
OE1 E:GLU26 2.6 41.3 1.0
OE2 E:GLU26 2.9 65.1 1.0
CD E:GLU26 3.0 54.3 1.0
C E:LYS22 3.5 31.9 1.0
CA E:ASP23 4.2 28.4 1.0
N E:ASP23 4.3 29.4 1.0
CG E:GLU26 4.5 38.3 1.0
CA E:LYS22 4.6 34.8 1.0
O E:HOH932 4.6 31.3 1.0
C E:ASP23 4.8 28.3 1.0
N E:PHE24 4.9 27.8 1.0
N E:ASP25 4.9 27.0 1.0
CB E:ASP25 5.0 27.2 1.0
CB E:LYS22 5.0 34.3 1.0

Calcium binding site 8 out of 8 in 3m81

Go back to Calcium Binding Sites List in 3m81
Calcium binding site 8 out of 8 in the Crystal Structure of Acetyl Xylan Esterase (TM0077) From Thermotoga Maritima at 2.50 A Resolution (Native Apo 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 2.50 A Resolution (Native Apo Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca406

b:72.8
occ:1.00
 O F:LYS22 2.6 34.3 1.0
OE2 F:GLU26 2.7 66.0 1.0
OE1 F:GLU26 2.8 53.2 1.0
O F:HOH741 3.1 38.0 1.0
CD F:GLU26 3.1 57.3 1.0
C F:LYS22 3.8 31.9 1.0
OD2 F:ASP25 4.5 32.2 1.0
CA F:ASP23 4.6 28.5 1.0
CG F:GLU26 4.6 47.6 1.0
N F:ASP23 4.7 29.4 1.0
CA F:LYS22 4.8 34.9 1.0
CB F:ASP25 4.9 27.2 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 13:28:24 2024

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