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Cadmium in PDB 2e0m: Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)

Enzymatic activity of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)

All present enzymatic activity of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L):
3.1.27.5;

Protein crystallography data

The structure of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L), PDB code: 2e0m was solved by H.Yamada, T.Tamada, M.Kosaka, R.Kuroki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 93.510, 93.510, 94.386, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.4

Other elements in 2e0m:

The structure of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) also contains other interesting chemical elements:

Chlorine (Cl) 11 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) (pdb code 2e0m). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L), PDB code: 2e0m:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 2e0m

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Cadmium binding site 1 out of 8 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:14.8
occ:0.50
 OE2 A:GLU125 2.3 30.8 1.0
OE1 A:GLU125 2.7 34.1 1.0
CD A:GLU125 2.8 32.3 1.0
NH2 A:ARG104 4.2 34.4 1.0
CG A:GLU125 4.3 34.3 1.0
NH1 A:ARG104 4.3 32.6 1.0
O A:HOH2146 4.4 34.5 1.0
CZ A:ARG104 4.7 34.2 1.0
CB A:GLU125 5.0 35.0 1.0

Cadmium binding site 2 out of 8 in 2e0m

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Cadmium binding site 2 out of 8 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:18.4
occ:0.50
 O A:HOH2090 2.2 26.0 1.0
CL A:CL2001 2.4 27.9 1.0
CL A:CL2002 2.4 20.6 1.0
O A:SER123 4.0 32.9 1.0
NE A:ARG104 4.3 33.0 1.0
O A:HOH2116 4.8 43.9 1.0
CA A:VAL124 4.9 34.3 1.0
C A:SER123 4.9 35.1 1.0
NH2 A:ARG104 4.9 34.4 1.0

Cadmium binding site 3 out of 8 in 2e0m

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Cadmium binding site 3 out of 8 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1003

b:18.2
occ:0.50
 O B:HOH2032 2.2 26.3 1.0
CL B:CL2003 2.8 27.8 1.0
CL B:CL2004 2.8 21.3 1.0
NE B:ARG104 4.1 33.9 1.0
O B:HOH2111 4.2 43.1 1.0
O B:SER123 4.2 33.2 1.0
NZ B:LYS102 4.2 41.8 1.0
NH2 B:ARG104 4.7 34.7 1.0
CD B:ARG104 4.8 32.9 1.0
CZ B:ARG104 4.9 33.3 1.0
OG B:SER123 4.9 40.1 1.0

Cadmium binding site 4 out of 8 in 2e0m

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Cadmium binding site 4 out of 8 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:49.5
occ:1.00
 CL A:CL2006 2.6 31.8 1.0
CL A:CL2005 2.7 45.2 1.0
O A:HOH2108 3.2 40.4 1.0
O A:HOH2111 3.5 30.4 1.0
CB A:SER100 3.8 33.2 1.0
OG A:SER100 3.8 38.7 1.0
O A:HOH2073 4.1 42.9 1.0
CD A:ARG85 4.3 37.7 1.0

Cadmium binding site 5 out of 8 in 2e0m

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Cadmium binding site 5 out of 8 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1005

b:34.9
occ:1.00
 ND1 B:HIS80 2.1 35.5 1.0
CL B:CL2007 2.3 35.2 1.0
OE1 B:GLU49 2.4 34.8 1.0
O B:HOH2129 2.5 35.6 1.0
CL B:CL2008 2.6 57.7 1.0
CE1 B:HIS80 2.8 32.6 1.0
OE2 B:GLU49 3.0 34.8 1.0
CD B:GLU49 3.1 34.9 1.0
CG B:HIS80 3.2 32.5 1.0
CB B:HIS80 3.8 29.3 1.0
O B:HIS48 4.0 31.9 1.0
NE2 B:HIS80 4.1 36.4 1.0
N B:HIS80 4.1 30.5 1.0
O B:HOH2021 4.2 20.3 1.0
CD2 B:HIS80 4.3 33.7 1.0
O B:HOH2131 4.3 50.3 1.0
O B:HOH2124 4.4 46.8 1.0
CG B:GLU49 4.5 33.5 1.0
O B:HOH2108 4.6 38.4 1.0
CA B:HIS80 4.6 31.3 1.0
O B:HOH2061 5.0 36.2 1.0
O B:HOH2145 5.0 59.9 1.0

Cadmium binding site 6 out of 8 in 2e0m

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Cadmium binding site 6 out of 8 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1006

b:91.9
occ:1.00
 ND1 A:HIS119 2.4 43.3 1.0
CL A:CL2009 2.7 44.6 1.0
CE1 A:HIS119 3.2 42.8 1.0
O A:HOH2157 3.5 67.5 1.0
CG A:HIS119 3.6 40.3 1.0
O A:HOH2128 3.9 44.1 1.0
CB A:HIS119 4.0 37.1 1.0
O A:HOH2074 4.1 45.0 1.0
CA A:HIS119 4.3 36.1 1.0
O A:HOH2072 4.4 43.7 1.0
NE2 A:HIS119 4.4 43.4 1.0
O A:HOH2087 4.6 25.2 1.0
N A:PHE120 4.6 34.8 1.0
CD2 A:HIS119 4.6 41.7 1.0
O A:PHE120 4.8 35.4 1.0
C A:HIS119 4.9 35.5 1.0
O A:VAL118 4.9 35.7 1.0

Cadmium binding site 7 out of 8 in 2e0m

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Cadmium binding site 7 out of 8 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1007

b:88.6
occ:1.00
 ND1 B:HIS119 2.4 42.0 1.0
CL B:CL2010 2.7 47.1 1.0
O B:HOH2195 2.8 48.7 1.0
O B:HOH2160 3.1 60.6 1.0
CE1 B:HIS119 3.3 42.3 1.0
CG B:HIS119 3.4 39.7 1.0
O B:HOH2135 3.7 50.9 1.0
O B:HOH2093 3.7 41.2 1.0
CB B:HIS119 3.8 36.8 1.0
CA B:HIS119 4.1 36.1 1.0
O B:HOH2141 4.2 48.5 1.0
O B:HOH2192 4.2 68.4 1.0
NE2 B:HIS119 4.4 41.8 1.0
N B:PHE120 4.5 35.0 1.0
O B:HOH2043 4.5 26.5 1.0
CD2 B:HIS119 4.5 40.7 1.0
C B:HIS119 4.8 35.5 1.0
O B:PHE120 4.8 35.5 1.0
O B:VAL118 4.8 35.7 1.0
O B:HOH2173 4.8 72.6 1.0
O B:HOH2164 5.0 49.4 1.0

Cadmium binding site 8 out of 8 in 2e0m

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Cadmium binding site 8 out of 8 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1008

b:34.9
occ:1.00
 ND1 A:HIS80 2.1 35.3 1.0
CL A:CL2011 2.3 34.0 1.0
O A:HOH2140 2.3 33.5 1.0
O A:HOH2138 2.4 30.8 1.0
OE1 A:GLU49 2.4 35.4 1.0
O A:HOH2142 2.6 33.1 1.0
CE1 A:HIS80 2.8 31.4 1.0
OE2 A:GLU49 3.0 34.5 1.0
CD A:GLU49 3.1 36.1 1.0
CG A:HIS80 3.2 32.3 1.0
CB A:HIS80 3.8 29.5 1.0
NE2 A:HIS80 4.0 36.9 1.0
O A:HIS48 4.0 31.9 1.0
N A:HIS80 4.1 30.2 1.0
CD2 A:HIS80 4.2 33.2 1.0
O A:HOH2018 4.3 21.2 1.0
O A:HOH2156 4.3 45.6 1.0
CG A:GLU49 4.5 34.0 1.0
O A:HOH2096 4.6 40.8 1.0
CA A:HIS80 4.6 30.9 1.0
O A:HOH2129 4.6 41.5 1.0

Reference:

H.Yamada, T.Tamada, M.Kosaka, K.Miyata, S.Fujiki, M.Tano, M.Moriya, M.Yamanishi, E.Honjo, H.Tada, T.Ino, H.Yamaguchi, J.Futami, M.Seno, T.Nomoto, T.Hirata, M.Yoshimura, R.Kuroki. 'Crystal Lattice Engineering,' An Approach to Engineer Protein Crystal Contacts By Creating Intermolecular Symmetry: Crystallization and Structure Determination of A Mutant Human Rnase 1 with A Hydrophobic Interface of Leucines Protein Sci. V. 16 1389 2007.
ISSN: ISSN 0961-8368
PubMed: 17586772
DOI: 10.1110/PS.072851407
Page generated: Fri Jul 19 14:46:42 2024

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