Atomistry » Calcium » PDB 3m0c-3mip » 3m83
Atomistry »
  Calcium »
    PDB 3m0c-3mip »
      3m83 »

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

Go back to Calcium Binding Sites List in 3m83
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

Go back to Calcium Binding Sites List in 3m83
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

Go back to Calcium Binding Sites List in 3m83
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

Go back to Calcium Binding Sites List in 3m83
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

Go back to Calcium Binding Sites List in 3m83
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

Go back to Calcium Binding Sites List in 3m83
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

Go back to Calcium Binding Sites List in 3m83
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

Go back to Calcium Binding Sites List in 3m83
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy