Atomistry » Cadmium » PDB 5an6-5gu0 » 5cax
Atomistry »
  Cadmium »
    PDB 5an6-5gu0 »
      5cax »

Cadmium in PDB 5cax: Crystal Structure of Methanosarcina Acetivorans Methanoredoxin

Protein crystallography data

The structure of Crystal Structure of Methanosarcina Acetivorans Methanoredoxin, PDB code: 5cax was solved by N.H.Yennawar, H.P.Yennawar, G.J.Ferry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.49 / 2.45
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 59.154, 59.154, 172.978, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 27.2

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Methanosarcina Acetivorans Methanoredoxin (pdb code 5cax). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the Crystal Structure of Methanosarcina Acetivorans Methanoredoxin, PDB code: 5cax:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in 5cax

Go back to Cadmium Binding Sites List in 5cax
Cadmium binding site 1 out of 12 in the Crystal Structure of Methanosarcina Acetivorans Methanoredoxin


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 Methanosarcina Acetivorans Methanoredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:54.8
occ:1.00
 OD1 A:ASP18 2.6 63.2 1.0
OD2 A:ASP18 2.9 64.9 1.0
OD1 B:ASP7 3.0 63.3 1.0
O A:HOH320 3.0 30.0 1.0
CG A:ASP18 3.1 65.5 1.0
CG B:ASP7 3.4 65.7 1.0
OD2 B:ASP7 3.5 64.3 1.0
OD1 A:ASP46 3.9 57.5 1.0
CD A:CD202 4.0 55.2 1.0
CG A:ASP46 4.1 55.9 1.0
O B:HOH311 4.1 59.5 1.0
OD2 A:ASP46 4.1 55.7 1.0
OG1 B:THR8 4.3 63.4 1.0
NZ B:LYS21 4.4 52.8 1.0
O A:HOH308 4.4 58.6 1.0
CB B:ASP7 4.5 68.6 1.0
CB A:ASP18 4.5 62.5 1.0
O B:HOH316 4.7 62.2 1.0
N B:THR8 4.8 66.6 1.0
CB A:ASP46 4.9 55.4 1.0
OD2 B:ASP9 5.0 55.4 1.0

Cadmium binding site 2 out of 12 in 5cax

Go back to Cadmium Binding Sites List in 5cax
Cadmium binding site 2 out of 12 in the Crystal Structure of Methanosarcina Acetivorans Methanoredoxin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Methanosarcina Acetivorans Methanoredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:55.2
occ:1.00
 OD1 A:ASP46 2.6 57.5 1.0
O A:HOH320 2.6 30.0 1.0
CE A:LYS12 2.8 59.8 1.0
OD2 A:ASP46 2.9 55.7 1.0
O B:HOH316 3.0 62.2 1.0
CG A:ASP46 3.1 55.9 1.0
NZ A:LYS12 3.5 57.2 1.0
CG1 A:VAL14 3.8 93.3 1.0
CD A:CD201 4.0 54.8 1.0
CD A:LYS12 4.2 60.7 1.0
O A:SER15 4.4 71.8 1.0
O A:HOH301 4.4 39.6 1.0
CB A:ASP46 4.6 55.4 1.0
OD1 B:ASP7 4.8 63.3 1.0
OD2 B:ASP9 4.8 55.4 1.0
O A:HOH310 4.8 37.8 1.0
O A:VAL14 4.8 95.1 1.0
CB A:VAL14 4.9 91.3 1.0
OD2 B:ASP7 4.9 64.3 1.0
OD1 B:ASP9 4.9 61.5 1.0
O A:HOH325 5.0 41.6 1.0

Cadmium binding site 3 out of 12 in 5cax

Go back to Cadmium Binding Sites List in 5cax
Cadmium binding site 3 out of 12 in the Crystal Structure of Methanosarcina Acetivorans Methanoredoxin


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 Methanosarcina Acetivorans Methanoredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:69.7
occ:1.00
 O A:PHE76 2.6 53.5 1.0
SG A:CYS30 2.7 68.6 1.0
SG A:CYS33 2.9 57.9 1.0
C A:PHE76 3.3 50.3 1.0
CB A:CYS30 3.4 72.3 1.0
CD A:PRO77 3.8 49.0 1.0
CB A:CYS33 3.8 58.4 1.0
N A:PRO77 3.8 50.9 1.0
N A:CYS33 4.0 59.0 1.0
CB A:PHE76 4.2 48.7 1.0
CA A:PHE76 4.3 49.7 1.0
CA A:CYS33 4.4 58.1 1.0
O A:HOH311 4.4 48.2 1.0
CA A:CYS30 4.8 66.9 1.0
N A:PHE76 4.8 53.6 1.0
C A:TRP32 4.9 60.4 1.0
CD1 A:LEU27 4.9 60.7 1.0

Cadmium binding site 4 out of 12 in 5cax

Go back to Cadmium Binding Sites List in 5cax
Cadmium binding site 4 out of 12 in the Crystal Structure of Methanosarcina Acetivorans Methanoredoxin


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 Methanosarcina Acetivorans Methanoredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:55.5
occ:1.00
 OD1 B:ASP46 2.4 50.9 1.0
O A:HOH323 2.7 41.0 1.0
O B:HOH320 2.7 44.9 1.0
OD2 B:ASP46 3.0 54.2 1.0
CG B:ASP46 3.0 54.6 1.0
CE B:LYS12 3.1 52.3 1.0
NZ B:LYS12 3.2 48.9 1.0
N B:SER15 3.5 83.7 1.0
CA B:VAL14 3.9 59.4 1.0
CD B:CD202 4.0 50.3 1.0
O B:HIS13 4.1 54.3 1.0
C B:VAL14 4.1 63.3 1.0
CA B:SER15 4.3 82.6 1.0
CB B:SER15 4.4 80.5 1.0
O A:HOH326 4.4 51.8 1.0
OD1 A:ASP9 4.5 63.3 1.0
CB B:ASP46 4.5 49.7 1.0
CB B:VAL14 4.6 60.0 1.0
CD B:LYS12 4.6 52.2 1.0
CG2 B:VAL14 4.6 62.7 1.0
O B:HOH307 4.7 46.0 1.0
OD2 A:ASP7 4.7 56.1 1.0
CG1 B:VAL14 4.7 59.5 1.0
C B:HIS13 4.7 59.5 1.0
N B:VAL14 4.8 57.3 1.0
OG B:SER15 4.9 79.4 1.0

Cadmium binding site 5 out of 12 in 5cax

Go back to Cadmium Binding Sites List in 5cax
Cadmium binding site 5 out of 12 in the Crystal Structure of Methanosarcina Acetivorans Methanoredoxin


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 Methanosarcina Acetivorans Methanoredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:50.3
occ:1.00
 OD2 B:ASP18 2.5 54.6 1.0
CB B:SER15 2.7 80.5 1.0
OG1 A:THR8 2.9 51.0 1.0
O B:HOH320 3.0 44.9 1.0
OD1 B:ASP18 3.0 56.0 1.0
OD2 A:ASP7 3.0 56.1 1.0
CG B:ASP18 3.1 62.7 1.0
OG B:SER15 3.6 79.4 1.0
CA B:SER15 3.7 82.6 1.0
N A:THR8 4.0 62.5 1.0
OD1 B:ASP46 4.0 50.9 1.0
CD B:CD201 4.0 55.5 1.0
CG A:ASP7 4.1 56.4 1.0
OD1 A:ASP9 4.2 63.3 1.0
CB A:THR8 4.2 64.8 1.0
CG B:ASP46 4.3 54.6 1.0
N B:SER15 4.3 83.7 1.0
CE A:LYS6 4.5 0.9 1.0
NZ A:LYS21 4.5 51.5 1.0
CB B:ASP18 4.5 56.1 1.0
CA A:THR8 4.6 57.6 1.0
NZ A:LYS6 4.6 0.3 1.0
OD2 B:ASP46 4.6 54.2 1.0
CB A:ASP7 4.7 58.0 1.0
CG2 A:THR8 4.7 70.0 1.0
CA A:ASP7 4.8 62.8 1.0
O B:HOH302 4.8 57.6 1.0
C B:SER15 4.9 84.3 1.0
O A:HOH323 4.9 41.0 1.0
CB B:ASP46 4.9 49.7 1.0
C A:ASP7 4.9 62.5 1.0
C A:THR8 5.0 52.9 1.0
O B:SER15 5.0 83.9 1.0

Cadmium binding site 6 out of 12 in 5cax

Go back to Cadmium Binding Sites List in 5cax
Cadmium binding site 6 out of 12 in the Crystal Structure of Methanosarcina Acetivorans Methanoredoxin


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 Methanosarcina Acetivorans Methanoredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd203

b:78.0
occ:0.75
 SG B:CYS30 2.8 83.8 1.0
O B:PHE76 2.9 73.3 1.0
SG B:CYS33 2.9 68.4 1.0
O3 B:SO4204 3.3 71.6 0.8
CB B:CYS30 3.3 76.2 1.0
C B:PHE76 3.4 70.7 1.0
CB B:CYS33 3.8 72.0 1.0
N B:PRO77 3.9 67.7 1.0
N B:CYS33 4.0 72.3 1.0
O4 B:SO4204 4.0 74.4 0.8
CB B:PHE76 4.0 68.0 1.0
CD B:PRO77 4.1 62.8 1.0
S B:SO4204 4.2 73.8 0.8
CA B:PHE76 4.3 69.0 1.0
CA B:CYS33 4.4 71.1 1.0
CA B:CYS30 4.8 76.6 1.0
CB B:TRP32 4.8 83.4 1.0
C B:TRP32 4.8 79.9 1.0
N B:PHE76 4.9 69.8 1.0

Cadmium binding site 7 out of 12 in 5cax

Go back to Cadmium Binding Sites List in 5cax
Cadmium binding site 7 out of 12 in the Crystal Structure of Methanosarcina Acetivorans Methanoredoxin


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 Methanosarcina Acetivorans Methanoredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd201

b:55.1
occ:1.00
 OD2 C:ASP18 2.6 55.9 1.0
OD1 C:ASP18 2.8 63.0 1.0
OD2 D:ASP7 3.0 68.9 1.0
CG C:ASP18 3.0 58.7 1.0
CG D:ASP7 3.2 66.9 1.0
O C:HOH321 3.5 34.2 1.0
OD1 D:ASP7 3.6 65.9 1.0
O D:HOH305 3.6 38.6 1.0
OD1 C:ASP46 3.9 54.4 1.0
CB D:ASP7 3.9 62.0 1.0
CD C:CD202 4.0 54.3 1.0
CG C:ASP46 4.1 53.9 1.0
OG1 D:THR8 4.2 60.1 1.0
OD2 C:ASP46 4.3 58.3 1.0
OD1 D:ASP9 4.4 64.4 1.0
N D:THR8 4.5 58.4 1.0
CB C:ASP18 4.5 57.5 1.0
O D:HOH301 4.6 44.2 1.0
O C:GLY16 4.7 64.3 1.0
CA D:ASP7 4.8 58.5 1.0
CB C:ASP46 4.8 56.2 1.0
O C:HOH303 4.9 47.0 1.0

Cadmium binding site 8 out of 12 in 5cax

Go back to Cadmium Binding Sites List in 5cax
Cadmium binding site 8 out of 12 in the Crystal Structure of Methanosarcina Acetivorans Methanoredoxin


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 Methanosarcina Acetivorans Methanoredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd202

b:54.3
occ:1.00
 OD1 C:ASP46 2.5 54.4 1.0
O C:HOH321 2.5 34.2 1.0
OD2 C:ASP46 2.8 58.3 1.0
CG C:ASP46 3.0 53.9 1.0
O C:HOH324 3.1 30.0 1.0
OG C:SER15 3.6 73.1 1.0
CA C:SER15 3.9 73.7 1.0
CD C:CD201 4.0 55.1 1.0
OD2 D:ASP7 4.1 68.9 1.0
CB C:SER15 4.2 72.9 1.0
CB C:ASP46 4.5 56.2 1.0
OD1 D:ASP9 4.5 64.4 1.0
O C:HOH303 4.6 47.0 1.0
C C:SER15 4.7 76.8 1.0
N C:SER15 4.9 77.1 1.0
OD2 D:ASP9 5.0 59.1 1.0

Cadmium binding site 9 out of 12 in 5cax

Go back to Cadmium Binding Sites List in 5cax
Cadmium binding site 9 out of 12 in the Crystal Structure of Methanosarcina Acetivorans Methanoredoxin


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 Methanosarcina Acetivorans Methanoredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd203

b:74.9
occ:1.00
 O C:PHE76 2.6 68.0 1.0
SG C:CYS33 2.8 63.9 1.0
SG C:CYS30 2.9 94.0 1.0
C C:PHE76 3.3 65.7 1.0
CB C:CYS30 3.4 74.8 1.0
CD C:PRO77 3.7 50.6 1.0
N C:PRO77 3.8 52.9 1.0
CB C:CYS33 3.8 57.8 1.0
N C:CYS33 3.8 54.2 1.0
CA C:CYS33 4.2 58.3 1.0
CB C:PHE76 4.2 68.6 1.0
CA C:PHE76 4.3 67.7 1.0
C C:TRP32 4.7 58.3 1.0
CB C:TRP32 4.7 59.5 1.0
CA C:CYS30 4.8 75.1 1.0
N C:PHE76 4.8 70.1 1.0

Cadmium binding site 10 out of 12 in 5cax

Go back to Cadmium Binding Sites List in 5cax
Cadmium binding site 10 out of 12 in the Crystal Structure of Methanosarcina Acetivorans Methanoredoxin


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 Methanosarcina Acetivorans Methanoredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd201

b:50.3
occ:1.00
 O D:HOH303 2.4 32.3 1.0
OD1 D:ASP46 2.5 56.3 1.0
OD2 D:ASP46 2.5 50.2 1.0
O D:HOH324 2.6 44.0 1.0
O D:HOH322 2.8 38.4 1.0
CG D:ASP46 2.8 52.8 1.0
CE D:LYS12 3.1 74.8 1.0
CD D:LYS12 3.7 74.5 1.0
O D:VAL14 4.0 86.8 1.0
O D:HIS13 4.0 90.2 1.0
CD D:CD202 4.0 50.0 1.0
NZ D:LYS12 4.1 73.3 1.0
CA D:VAL14 4.1 92.1 1.0
C D:VAL14 4.1 91.3 1.0
OD2 C:ASP7 4.1 72.5 1.0
CB D:ASP46 4.3 49.5 1.0
C D:HIS13 4.6 91.3 1.0
N D:VAL14 4.7 94.4 1.0
CG D:LYS12 4.8 76.7 1.0
N D:SER15 4.9 0.9 1.0

Reference:

D.Yenugudhati, D.Prakash, A.K.Kumar, R.S.Kumar, N.H.Yennawar, H.P.Yennawar, J.G.Ferry. Structural and Biochemical Characterizations of Methanoredoxin From Methanosarcina Acetivorans, A Glutaredoxin-Like Enzyme with Coenzyme M-Dependent Protein Disulfide Reductase Activity. Biochemistry V. 55 313 2016.
ISSN: ISSN 0006-2960
PubMed: 26684934
DOI: 10.1021/ACS.BIOCHEM.5B00823
Page generated: Sat Dec 12 08:26:23 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy