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Cadmium in PDB 3ng1: N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus

Protein crystallography data

The structure of N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus, PDB code: 3ng1 was solved by D.M.Freymann, R.M.Stroud, P.Walter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.310, 99.010, 99.830, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 22.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus (pdb code 3ng1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus, PDB code: 3ng1:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 3ng1

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Cadmium binding site 1 out of 6 in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd701

b:26.9
occ:1.00
OD2 B:ASP50 2.3 26.1 1.0
OE2 B:GLU46 2.3 28.2 1.0
OE2 A:GLU33 2.4 27.3 1.0
OE1 A:GLU33 2.4 25.4 1.0
OE2 A:GLU11 2.4 31.4 1.0
OE1 A:GLU11 2.5 27.3 1.0
CD A:GLU33 2.7 28.7 1.0
CD A:GLU11 2.8 33.2 1.0
OD1 B:ASP50 2.8 26.7 1.0
CG B:ASP50 2.9 21.5 1.0
CD B:GLU46 3.4 32.1 1.0
CG B:GLU46 3.7 25.8 1.0
CD A:ARG15 4.1 14.7 1.0
CG A:GLU33 4.1 27.4 1.0
NH1 A:ARG15 4.2 19.9 1.0
CG A:GLU11 4.3 22.9 1.0
CB B:ASP50 4.3 21.9 1.0
O A:HOH993 4.4 36.9 1.0
O B:HOH972 4.4 20.2 1.0
O A:HOH973 4.5 17.7 1.0
OE1 B:GLU46 4.5 31.3 1.0
O B:HOH975 4.7 47.8 1.0
O B:HOH1060 4.8 40.6 1.0
O B:GLU46 4.8 24.4 1.0
O B:HOH1059 4.8 47.3 1.0
NE A:ARG15 4.8 17.3 1.0
CZ A:ARG15 4.9 15.5 1.0
CG A:ARG15 5.0 13.1 1.0

Cadmium binding site 2 out of 6 in 3ng1

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Cadmium binding site 2 out of 6 in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd702

b:37.3
occ:0.50
OE2 A:GLU285 2.3 44.9 1.0
OE1 A:GLU285 2.6 38.9 1.0
CD A:GLU285 2.7 35.5 1.0
O A:HOH1060 4.1 48.0 1.0
CG A:GLU285 4.3 24.9 1.0
NZ A:LYS83 4.4 21.6 1.0
O A:HOH1048 4.5 37.4 1.0
O A:HOH1023 4.6 33.7 1.0

Cadmium binding site 3 out of 6 in 3ng1

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Cadmium binding site 3 out of 6 in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd703

b:26.2
occ:0.50
NE2 A:HIS261 2.4 25.8 1.0
CE1 A:HIS261 3.4 26.0 1.0
CD2 A:HIS261 3.4 23.8 1.0
ND1 A:HIS261 4.5 23.7 1.0
CG A:HIS261 4.5 21.7 1.0
ND2 A:ASN44 4.6 33.0 1.0
OD1 A:ASN44 4.8 37.3 1.0
CB A:GLU46 4.8 25.2 1.0

Cadmium binding site 4 out of 6 in 3ng1

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Cadmium binding site 4 out of 6 in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd701

b:26.9
occ:1.00
OE2 B:GLU33 2.4 27.3 1.0
OE1 B:GLU33 2.4 25.4 1.0
OE2 B:GLU11 2.4 31.4 1.0
OE1 B:GLU11 2.5 27.3 1.0
CD B:GLU33 2.7 28.7 1.0
CD B:GLU11 2.8 33.2 1.0
CD B:ARG15 4.1 14.7 1.0
CG B:GLU33 4.1 27.4 1.0
NH1 B:ARG15 4.2 19.9 1.0
CG B:GLU11 4.3 22.9 1.0
O B:HOH1000 4.4 36.9 1.0
O B:HOH978 4.4 20.2 1.0
O B:HOH977 4.5 17.7 1.0
O B:HOH1024 4.7 47.8 1.0
NE B:ARG15 4.9 17.3 1.0
CZ B:ARG15 4.9 15.5 1.0
CG B:ARG15 5.0 13.1 1.0

Cadmium binding site 5 out of 6 in 3ng1

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Cadmium binding site 5 out of 6 in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd702

b:37.3
occ:0.50
OE2 B:GLU285 2.3 44.9 1.0
OE1 B:GLU285 2.6 38.9 1.0
CD B:GLU285 2.7 35.5 1.0
O B:HOH1065 4.1 48.0 1.0
CG B:GLU285 4.3 24.9 1.0
NZ B:LYS83 4.4 21.6 1.0
O B:HOH1054 4.5 37.4 1.0
O B:HOH1030 4.6 33.7 1.0

Cadmium binding site 6 out of 6 in 3ng1

Go back to Cadmium Binding Sites List in 3ng1
Cadmium binding site 6 out of 6 in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd703

b:26.2
occ:0.50
NE2 B:HIS261 2.4 25.8 1.0
CE1 B:HIS261 3.4 26.0 1.0
CD2 B:HIS261 3.4 23.8 1.0
ND1 B:HIS261 4.5 23.7 1.0
CG B:HIS261 4.5 21.7 1.0
ND2 B:ASN44 4.6 33.0 1.0
OD1 B:ASN44 4.8 37.3 1.0
CB B:GLU46 4.8 25.2 1.0

Reference:

D.M.Freymann, R.J.Keenan, R.M.Stroud, P.Walter. Functional Changes in the Structure of the Srp Gtpase on Binding Gdp and MG2+Gdp. Nat.Struct.Biol. V. 6 793 1999.
ISSN: ISSN 1072-8368
PubMed: 10426959
DOI: 10.1038/11572
Page generated: Fri Aug 28 13:49:30 2020
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