Atomistry » Calcium » PDB 3m0c-3mip » 3m81
Atomistry »
  Calcium »
    PDB 3m0c-3mip »
      3m81 »

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

Go back to Calcium Binding Sites List in 3m81
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

Go back to Calcium Binding Sites List in 3m81
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

Go back to Calcium Binding Sites List in 3m81
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

Go back to Calcium Binding Sites List in 3m81
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy