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Cadmium in PDB 1m5q: Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum

Protein crystallography data

The structure of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum, PDB code: 1m5q was solved by C.Mura, M.Phillips, A.Kozhukhovsky, D.Eisenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.322, 172.427, 148.108, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.6

Other elements in 1m5q:

The structure of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum also contains other interesting chemical elements:

Sodium (Na) 5 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum (pdb code 1m5q). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 28 binding sites of Cadmium where determined in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum, PDB code: 1m5q:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 28 in 1m5q

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Cadmium binding site 1 out of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2001

b:35.5
occ:0.93
NE2 A:HIS39 2.3 24.4 1.0
O B:HOH3008 2.5 24.3 1.0
O A:HOH4034 2.6 11.3 1.0
O A:HOH4055 2.7 29.4 1.0
OE1 B:GLU84 2.7 43.9 1.0
OE2 B:GLU84 3.0 45.2 1.0
CD B:GLU84 3.0 41.7 1.0
CD2 A:HIS39 3.1 20.5 1.0
CE1 A:HIS39 3.3 23.1 1.0
O B:HOH3032 3.9 32.6 1.0
CG B:GLU15 4.1 31.9 1.0
NE A:ARG62 4.1 31.2 1.0
CG B:GLU84 4.2 38.6 1.0
CG A:HIS39 4.3 22.2 1.0
ND1 A:HIS39 4.4 22.7 1.0
OE2 B:GLU15 4.5 37.4 1.0
NH2 A:ARG62 4.6 28.8 1.0
CZ A:ARG62 4.8 30.6 1.0
CD B:GLU15 4.9 34.9 1.0
O B:HOH3060 4.9 42.4 1.0

Cadmium binding site 2 out of 28 in 1m5q

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Cadmium binding site 2 out of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2007

b:37.4
occ:1.02
NE2 G:HIS39 2.1 25.7 1.0
O G:HOH4058 2.5 39.6 1.0
OE1 A:GLU84 2.5 43.4 1.0
O G:HOH4003 2.6 16.0 1.0
OE2 A:GLU84 2.8 43.7 1.0
CD A:GLU84 2.9 42.4 1.0
CD2 G:HIS39 3.1 25.1 1.0
CE1 G:HIS39 3.1 24.6 1.0
O G:HOH4059 4.0 46.8 1.0
CG A:GLU15 4.1 32.8 1.0
O A:HOH4041 4.1 38.0 1.0
NE G:ARG62 4.2 28.6 1.0
ND1 G:HIS39 4.2 23.7 1.0
CG G:HIS39 4.2 27.8 1.0
CG A:GLU84 4.4 37.8 1.0
NH2 G:ARG62 4.5 28.9 1.0
OE1 A:GLU15 4.8 37.0 1.0
CZ G:ARG62 4.8 30.5 1.0

Cadmium binding site 3 out of 28 in 1m5q

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Cadmium binding site 3 out of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2002

b:38.3
occ:0.91
NE2 B:HIS39 2.2 28.3 1.0
OE2 C:GLU84 2.3 43.5 1.0
OE1 C:GLU84 2.4 42.6 1.0
CD C:GLU84 2.7 42.8 1.0
O C:HOH194 2.7 46.0 1.0
O B:HOH3003 2.7 21.6 1.0
CD2 B:HIS39 3.1 23.8 1.0
CE1 B:HIS39 3.2 25.4 1.0
OE2 C:GLU15 3.8 52.6 1.0
NE B:ARG62 4.1 31.8 1.0
CG C:GLU84 4.2 40.9 1.0
O C:HOH177 4.2 36.9 1.0
ND1 B:HIS39 4.3 25.6 1.0
CG B:HIS39 4.3 25.7 1.0
CD C:GLU15 4.5 48.9 1.0
NH2 B:ARG62 4.6 28.2 1.0
CZ B:ARG62 4.8 29.3 1.0
OE1 C:GLU15 4.8 52.5 1.0
CD B:ARG62 4.9 29.2 1.0

Cadmium binding site 4 out of 28 in 1m5q

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Cadmium binding site 4 out of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd2003

b:44.8
occ:0.95
OE2 D:GLU84 2.4 37.3 1.0
OE1 D:GLU84 2.4 35.5 1.0
NE2 C:HIS39 2.4 31.1 1.0
O C:HOH144 2.5 23.3 1.0
CD D:GLU84 2.7 36.8 1.0
O C:HOH179 2.8 41.8 1.0
CD2 C:HIS39 3.1 28.7 1.0
CE1 C:HIS39 3.6 30.8 1.0
NE C:ARG62 4.0 30.2 1.0
O D:HOH2040 4.0 37.5 1.0
CG D:GLU15 4.2 39.3 1.0
CG D:GLU84 4.2 35.7 1.0
NH2 C:ARG62 4.3 30.1 1.0
CG C:HIS39 4.4 31.0 1.0
ND1 C:HIS39 4.6 33.4 1.0
CZ C:ARG62 4.6 31.5 1.0
OE1 D:GLU15 4.8 46.2 1.0
CD C:ARG62 5.0 30.1 1.0

Cadmium binding site 5 out of 28 in 1m5q

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Cadmium binding site 5 out of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd2004

b:44.1
occ:0.98
OE2 E:GLU84 2.2 38.6 1.0
NE2 D:HIS39 2.3 38.5 1.0
O E:HOH2029 2.4 46.7 1.0
OE1 E:GLU84 2.5 40.1 1.0
O D:HOH2005 2.6 18.0 1.0
CD E:GLU84 2.6 40.2 1.0
CD2 D:HIS39 3.1 34.5 1.0
CE1 D:HIS39 3.4 38.6 1.0
NE D:ARG62 4.0 26.1 1.0
CG E:GLU84 4.1 38.5 1.0
CG E:GLU15 4.2 38.5 1.0
CG D:HIS39 4.3 35.6 1.0
NH2 D:ARG62 4.4 26.5 1.0
ND1 D:HIS39 4.4 38.7 1.0
CZ D:ARG62 4.7 28.8 1.0
CD D:ARG62 5.0 26.4 1.0
OE1 E:GLU15 5.0 45.6 1.0

Cadmium binding site 6 out of 28 in 1m5q

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Cadmium binding site 6 out of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd2005

b:40.6
occ:1.00
NE2 E:HIS39 2.2 27.2 1.0
O F:HOH5073 2.5 38.2 1.0
OE2 F:GLU84 2.5 39.3 1.0
O E:HOH2008 2.5 15.4 1.0
OE1 F:GLU84 2.5 40.7 1.0
CD F:GLU84 2.8 40.9 1.0
CD2 E:HIS39 3.0 27.9 1.0
CE1 E:HIS39 3.3 30.2 1.0
O F:HOH5038 4.1 34.2 1.0
NE E:ARG62 4.1 31.3 1.0
CG E:HIS39 4.2 30.9 1.0
CG F:GLU15 4.2 32.0 1.0
CG F:GLU84 4.3 38.3 1.0
ND1 E:HIS39 4.4 29.8 1.0
NH2 E:ARG62 4.6 31.2 1.0
OE2 F:GLU15 4.7 40.5 1.0
CZ E:ARG62 4.9 32.7 1.0

Cadmium binding site 7 out of 28 in 1m5q

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Cadmium binding site 7 out of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cd2006

b:37.0
occ:0.97
NE2 F:HIS39 2.2 26.6 1.0
OE1 G:GLU84 2.3 42.7 1.0
O G:HOH4044 2.3 31.2 1.0
O F:HOH5049 2.5 32.4 1.0
OE2 G:GLU84 2.6 41.5 1.0
O F:HOH5016 2.6 14.2 1.0
CD G:GLU84 2.8 39.5 1.0
CD2 F:HIS39 3.0 23.3 1.0
CE1 F:HIS39 3.4 25.8 1.0
O G:HOH4062 4.0 46.3 1.0
NE F:ARG62 4.0 28.7 1.0
CG G:GLU15 4.1 36.7 1.0
O G:HOH4016 4.1 27.5 1.0
CG F:HIS39 4.2 25.8 1.0
CG G:GLU84 4.3 36.5 1.0
NH2 F:ARG62 4.3 27.1 1.0
ND1 F:HIS39 4.4 26.2 1.0
O F:HOH5056 4.7 37.8 1.0
CZ F:ARG62 4.7 30.6 1.0
OE1 G:GLU15 4.7 44.0 1.0
O G:HOH4028 4.8 37.0 1.0
CD G:GLU15 5.0 41.8 1.0

Cadmium binding site 8 out of 28 in 1m5q

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Cadmium binding site 8 out of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cd2008

b:38.6
occ:0.94
NE2 H:HIS39 2.4 29.2 1.0
O I:HOH5064 2.5 31.4 1.0
O H:HOH5061 2.6 38.0 1.0
O3 H:GOL4002 2.6 52.4 1.0
CD2 H:HIS39 3.3 26.4 1.0
C3 H:GOL4002 3.3 54.6 1.0
CE1 H:HIS39 3.4 27.1 1.0
OE1 I:GLU15 3.6 45.6 1.0
NZ G:LYS91 4.1 39.3 1.0
C2 H:GOL4002 4.2 56.1 1.0
CG H:HIS39 4.5 25.1 1.0
NH1 H:ARG62 4.5 29.0 1.0
ND1 H:HIS39 4.5 27.5 1.0
O H:HOH5034 4.7 37.6 1.0
CE G:LYS91 4.7 37.6 1.0
CD I:GLU15 4.7 43.0 1.0
O2 H:GOL4002 4.8 57.8 1.0
CD H:ARG62 4.8 23.6 1.0
O G:HOH4040 4.8 40.9 1.0

Cadmium binding site 9 out of 28 in 1m5q

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Cadmium binding site 9 out of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cd2014

b:40.8
occ:0.97
NE2 N:HIS39 2.3 25.5 1.0
OE2 H:GLU15 2.6 33.1 1.0
O N:HOH5038 2.7 30.1 1.0
CD2 N:HIS39 3.1 23.2 1.0
CD H:GLU15 3.2 37.6 1.0
OE1 H:GLU15 3.2 38.6 1.0
CE1 N:HIS39 3.4 26.4 1.0
NH1 N:ARG62 4.3 23.7 1.0
CG N:HIS39 4.3 24.3 1.0
ND1 N:HIS39 4.4 25.8 1.0
CG H:GLU15 4.5 33.4 1.0
O A:HOH4049 4.6 37.3 1.0
CD N:ARG62 4.8 26.5 1.0
O A:HOH4052 4.9 40.0 1.0

Cadmium binding site 10 out of 28 in 1m5q

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Cadmium binding site 10 out of 28 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cd2009

b:46.1
occ:1.06
NE2 I:HIS39 2.3 32.9 1.0
OE1 J:GLU15 2.8 49.7 1.0
O I:HOH5045 2.8 40.4 1.0
OE2 J:GLU15 3.0 50.2 1.0
CD J:GLU15 3.1 46.4 1.0
CD2 I:HIS39 3.2 29.3 1.0
CE1 I:HIS39 3.3 32.6 1.0
CG J:GLU15 4.3 41.5 1.0
NH1 I:ARG62 4.4 32.5 1.0
CG I:HIS39 4.4 30.5 1.0
ND1 I:HIS39 4.4 32.9 1.0
O F:HOH5053 4.6 31.6 1.0
NZ F:LYS91 4.9 43.3 1.0
CD I:ARG62 4.9 30.7 1.0

Reference:

C.Mura, M.Phillips, A.Kozhukhovsky, D.Eisenberg. Structure and Assembly of An Augmented Sm-Like Archaeal Protein 14-Mer Proc.Natl.Acad.Sci.Usa V. 100 4539 2003.
ISSN: ISSN 0027-8424
PubMed: 12668760
DOI: 10.1073/PNAS.0538042100
Page generated: Sat Dec 12 08:10:57 2020

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