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Cadmium in PDB 3mmu: Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima

Protein crystallography data

The structure of Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima, PDB code: 3mmu was solved by J.H.Pereira, Z.Chen, R.P.Mcandrew, R.Sapra, S.R.Chhabra, K.L.Sale, B.A.Simmons, P.D.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.99 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 87.584, 95.791, 103.497, 64.08, 75.07, 68.73
R / Rfree (%) 20.5 / 21.8

Other elements in 3mmu:

The structure of Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima also contains other interesting chemical elements:

Nickel (Ni) 36 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima (pdb code 3mmu). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 20 binding sites of Cadmium where determined in the Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima, PDB code: 3mmu:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 20 in 3mmu

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Cadmium binding site 1 out of 20 in the Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd318

b:32.6
occ:1.00
 OE2 A:GLU98 2.1 24.4 1.0
ND1 A:HIS96 2.5 25.5 1.0
O A:HOH582 2.5 17.2 1.0
O B:HOH769 2.6 33.4 1.0
CD A:GLU98 2.8 27.0 1.0
OE1 A:GLU98 2.9 28.8 1.0
O A:HOH1316 3.4 44.5 1.0
CG A:HIS96 3.5 26.2 1.0
CE1 A:HIS96 3.5 23.4 1.0
CA A:HIS96 3.7 22.5 1.0
CB A:HIS96 3.9 24.0 1.0
CG A:GLU98 4.2 25.1 1.0
O A:HOH338 4.3 19.5 1.0
O B:HOH352 4.3 30.4 1.0
O A:HOH671 4.3 29.3 1.0
CE1 A:HIS138 4.5 26.3 1.0
N A:HIS96 4.5 20.6 1.0
NE2 A:HIS96 4.6 26.0 1.0
CD2 A:HIS96 4.7 22.1 1.0
C A:HIS96 4.7 23.6 1.0
NE2 A:HIS138 5.0 27.2 1.0
CG B:PRO25 5.0 28.7 1.0

Cadmium binding site 2 out of 20 in 3mmu

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Cadmium binding site 2 out of 20 in the Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd319

b:42.3
occ:1.00
 O A:HOH1368 2.2 18.9 1.0
O B:HOH1367 2.3 28.1 1.0
OE2 B:GLU99 2.5 34.2 1.0
OE2 A:GLU99 2.5 33.8 1.0
OE1 A:GLU99 2.8 26.5 1.0
O B:HOH1369 2.8 29.5 1.0
CD A:GLU99 3.0 23.1 1.0
OE1 B:GLU99 3.1 33.0 1.0
CD B:GLU99 3.2 30.5 1.0
CB A:GLU98 4.2 25.7 1.0
O B:HOH355 4.2 42.0 1.0
NH2 A:ARG55 4.5 26.8 1.0
CG A:GLU99 4.5 23.9 1.0
O A:HOH804 4.5 31.1 1.0
CG A:GLU98 4.5 25.1 1.0
CG2 B:THR58 4.6 27.8 1.0
CG B:GLU99 4.6 30.5 1.0
NH2 B:ARG55 4.6 31.5 1.0
CG2 A:THR58 4.6 23.6 1.0
CB B:GLU98 4.7 31.9 1.0
N A:GLU98 4.7 21.9 1.0
N A:GLU99 4.8 18.5 1.0
CA A:GLU98 5.0 23.4 1.0
CG B:GLU98 5.0 27.1 1.0

Cadmium binding site 3 out of 20 in 3mmu

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Cadmium binding site 3 out of 20 in the Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd320

b:50.3
occ:1.00
 OE2 A:GLU136 2.2 35.4 1.0
O A:HOH606 2.3 33.9 1.0
O A:HOH776 2.3 31.8 1.0
OE1 A:GLU253 2.3 33.3 1.0
O A:HOH596 2.4 27.8 1.0
O A:HOH1027 2.5 41.7 1.0
CD A:GLU136 3.0 31.8 1.0
OE1 A:GLU136 3.1 31.4 1.0
CD A:GLU253 3.3 28.0 1.0
OE2 A:GLU253 3.6 25.7 1.0
ND1 A:HIS196 4.0 28.4 1.0
OH A:TYR198 4.1 29.5 1.0
O A:HOH369 4.2 38.1 1.0
CE2 A:TYR198 4.2 32.0 1.0
CG A:GLU136 4.3 30.7 1.0
O A:HOH576 4.4 35.0 1.0
O A:HOH557 4.5 34.8 1.0
CZ A:TYR198 4.5 33.1 1.0
NI A:NI325 4.6 85.0 1.0
CG A:GLU253 4.6 32.1 1.0
CE1 A:HIS196 4.7 28.9 1.0
CB A:GLU253 4.9 30.6 1.0
CG A:HIS196 4.9 32.5 1.0
ND2 A:ASN135 4.9 24.0 1.0

Cadmium binding site 4 out of 20 in 3mmu

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Cadmium binding site 4 out of 20 in the Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd318

b:33.0
occ:1.00
 OE2 B:GLU98 2.1 31.9 1.0
O B:HOH584 2.5 21.4 1.0
ND1 B:HIS96 2.5 29.1 1.0
O A:HOH601 2.6 32.7 1.0
CD B:GLU98 2.7 28.6 1.0
OE1 B:GLU98 2.8 34.1 1.0
CG B:HIS96 3.5 26.8 1.0
CE1 B:HIS96 3.5 26.5 1.0
CA B:HIS96 3.7 29.0 1.0
CB B:HIS96 3.9 26.7 1.0
CG B:GLU98 4.2 27.1 1.0
O B:HOH766 4.2 28.6 1.0
O B:HOH643 4.2 35.5 1.0
O B:HOH420 4.3 39.8 1.0
O A:HOH393 4.3 24.9 1.0
N B:HIS96 4.4 28.1 1.0
CE1 B:HIS138 4.5 27.6 1.0
C B:HIS96 4.6 31.1 1.0
CD2 B:HIS96 4.6 26.7 1.0
NE2 B:HIS96 4.7 24.7 1.0
CG A:PRO25 4.7 27.2 1.0
NE2 B:HIS138 5.0 29.4 1.0

Cadmium binding site 5 out of 20 in 3mmu

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Cadmium binding site 5 out of 20 in the Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd319

b:53.0
occ:1.00
 O B:HOH775 2.2 53.2 1.0
OE1 B:GLU253 2.3 37.2 1.0
O B:HOH611 2.3 34.9 1.0
OE2 B:GLU136 2.3 33.8 1.0
O B:HOH1250 2.5 33.7 1.0
O B:HOH1249 2.6 44.2 1.0
CD B:GLU136 3.0 26.5 1.0
OE1 B:GLU136 3.2 27.7 1.0
CD B:GLU253 3.2 35.3 1.0
OE2 B:GLU253 3.5 26.8 1.0
ND1 B:HIS196 4.0 26.6 1.0
OH B:TYR198 4.1 36.5 1.0
CE2 B:TYR198 4.2 31.0 1.0
O B:HOH379 4.3 33.3 1.0
CG B:GLU136 4.3 24.6 1.0
O B:HOH1059 4.4 51.0 1.0
CZ B:TYR198 4.5 33.9 1.0
O B:HOH420 4.6 39.8 1.0
CG B:GLU253 4.6 32.3 1.0
CE1 B:HIS196 4.7 26.7 1.0
NI B:NI323 4.7 76.9 1.0
CB B:GLU253 4.9 33.2 1.0
ND2 B:ASN135 4.9 19.4 1.0
CG B:HIS196 5.0 30.9 1.0

Cadmium binding site 6 out of 20 in 3mmu

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Cadmium binding site 6 out of 20 in the Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd318

b:41.2
occ:1.00
 OE2 C:GLU98 2.2 32.8 1.0
O C:HOH586 2.3 38.5 1.0
ND1 C:HIS96 2.5 39.4 1.0
O C:HOH578 2.7 21.2 1.0
CD C:GLU98 2.8 34.7 1.0
OE1 C:GLU98 2.9 35.9 1.0
O C:HOH622 3.4 58.3 1.0
CG C:HIS96 3.5 36.9 1.0
CE1 C:HIS96 3.5 35.5 1.0
CA C:HIS96 3.6 33.2 1.0
O D:HOH784 3.7 53.5 1.0
CB C:HIS96 3.9 34.9 1.0
O C:HOH1031 4.0 52.7 1.0
O C:HOH346 4.2 31.6 1.0
CG C:GLU98 4.2 33.0 1.0
N C:HIS96 4.4 36.3 1.0
CE1 C:HIS138 4.5 28.8 1.0
C C:HIS96 4.6 34.0 1.0
CD2 C:HIS96 4.6 33.9 1.0
NE2 C:HIS96 4.6 38.9 1.0
O D:HOH330 4.7 29.6 1.0
NE2 C:HIS138 5.0 32.8 1.0

Cadmium binding site 7 out of 20 in 3mmu

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Cadmium binding site 7 out of 20 in the Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd319

b:53.4
occ:1.00
 OE2 D:GLU99 2.2 35.7 1.0
O C:HOH1371 2.4 31.4 1.0
OE2 C:GLU99 2.4 38.9 1.0
OE1 D:GLU99 2.6 30.3 1.0
O C:HOH1370 2.7 42.4 1.0
CD D:GLU99 2.7 30.2 1.0
O D:HOH1372 2.7 48.2 1.0
OE1 C:GLU99 2.9 38.3 1.0
CD C:GLU99 3.1 37.4 1.0
CG D:GLU99 4.2 31.7 1.0
O C:HOH1373 4.2 56.0 1.0
CB D:GLU98 4.3 31.9 1.0
CG2 C:THR58 4.5 26.9 1.0
CG C:GLU99 4.6 32.5 1.0
CB C:GLU98 4.7 34.5 1.0
NH2 C:ARG55 4.7 25.8 1.0
N D:GLU99 4.7 26.5 1.0
CG D:GLU98 4.7 30.3 1.0
NH2 D:ARG55 4.8 32.6 1.0
N D:GLU98 4.9 25.5 1.0
CG2 D:THR58 4.9 28.9 1.0
CG C:GLU98 5.0 33.0 1.0

Cadmium binding site 8 out of 20 in 3mmu

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Cadmium binding site 8 out of 20 in the Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd320

b:63.7
occ:1.00
 OE2 C:GLU136 2.2 42.5 1.0
OE1 C:GLU253 2.3 48.7 1.0
O C:HOH623 2.3 47.1 1.0
O C:HOH598 2.4 38.1 1.0
O C:HOH501 2.4 40.0 1.0
CD C:GLU136 3.0 36.5 1.0
OE1 C:GLU136 3.1 38.5 1.0
CD C:GLU253 3.3 43.6 1.0
OE2 C:GLU253 3.5 37.6 1.0
ND1 C:HIS196 4.0 38.7 1.0
OH C:TYR198 4.1 45.4 1.0
CE2 C:TYR198 4.1 47.1 1.0
CG C:GLU136 4.3 36.5 1.0
O C:HOH1026 4.4 56.0 1.0
O C:HOH502 4.4 35.1 1.0
CZ C:TYR198 4.5 48.6 1.0
CG C:GLU253 4.6 41.8 1.0
CE1 C:HIS196 4.7 39.5 1.0
NI C:NI323 4.7 98.8 1.0
CB C:GLU253 4.9 41.8 1.0
CG C:HIS196 4.9 44.1 1.0
ND2 C:ASN135 5.0 29.3 1.0

Cadmium binding site 9 out of 20 in 3mmu

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Cadmium binding site 9 out of 20 in the Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd318

b:39.5
occ:1.00
 OE2 D:GLU98 2.1 34.7 1.0
O D:HOH592 2.6 33.0 1.0
ND1 D:HIS96 2.6 36.4 1.0
O D:HOH1241 2.6 16.5 1.0
CD D:GLU98 2.7 34.1 1.0
OE1 D:GLU98 2.8 40.8 1.0
CG D:HIS96 3.5 38.7 1.0
CE1 D:HIS96 3.6 39.9 1.0
CA D:HIS96 3.7 34.4 1.0
CB D:HIS96 3.9 33.5 1.0
CG D:GLU98 4.2 30.3 1.0
O D:HOH855 4.3 44.5 1.0
O D:HOH356 4.3 32.5 1.0
O D:HOH544 4.4 41.6 1.0
N D:HIS96 4.5 29.2 1.0
CE1 D:HIS138 4.5 34.1 1.0
C D:HIS96 4.6 32.9 1.0
O C:HOH928 4.7 29.0 1.0
CD2 D:HIS96 4.7 35.4 1.0
NE2 D:HIS96 4.7 38.1 1.0
CG C:PRO25 4.8 34.8 1.0
NE2 D:HIS138 4.9 36.7 1.0
O D:HOH892 5.0 41.7 1.0

Cadmium binding site 10 out of 20 in 3mmu

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Cadmium binding site 10 out of 20 in the Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd319

b:60.5
occ:1.00
 O D:HOH1011 2.2 36.1 1.0
O D:HOH1319 2.2 57.5 1.0
OE2 D:GLU136 2.3 41.9 1.0
OE1 D:GLU253 2.4 43.7 1.0
O D:HOH814 2.5 45.5 1.0
O D:HOH1252 2.6 52.6 1.0
CD D:GLU136 3.0 41.0 1.0
OE1 D:GLU136 3.1 39.7 1.0
CD D:GLU253 3.4 46.1 1.0
OE2 D:GLU253 3.6 40.8 1.0
O D:HOH341 4.1 55.0 1.0
ND1 D:HIS196 4.1 40.3 1.0
OH D:TYR198 4.1 43.3 1.0
O D:HOH800 4.2 37.9 1.0
CE2 D:TYR198 4.2 43.5 1.0
O D:HOH892 4.4 41.7 1.0
CG D:GLU136 4.4 36.0 1.0
NI D:NI322 4.4 0.6 1.0
CZ D:TYR198 4.6 46.5 1.0
CG D:GLU253 4.7 48.8 1.0
CE1 D:HIS196 4.8 36.5 1.0
O D:HOH855 4.8 44.5 1.0
ND2 D:ASN135 5.0 29.3 1.0
CB D:GLU253 5.0 47.8 1.0

Reference:

J.H.Pereira, Z.Chen, R.P.Mcandrew, R.Sapra, S.R.Chhabra, K.L.Sale, B.A.Simmons, P.D.Adams. Biochemical Characterization and Crystal Structure of Endoglucanase CEL5A From the Hyperthermophilic Thermotoga Maritima. J.Struct.Biol. V. 172 372 2010.
ISSN: ISSN 1047-8477
PubMed: 20599513
DOI: 10.1016/J.JSB.2010.06.018
Page generated: Sun Jan 24 09:55:53 2021

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