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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Fri Jul 19 18:15:18 2024

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