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Cadmium in PDB 2e0l: Mutant Human Ribonuclease 1 (Q28L, R31L, R32L)

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

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

Protein crystallography data

The structure of Mutant Human Ribonuclease 1 (Q28L, R31L, R32L), PDB code: 2e0l 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 / 1.60
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 93.376, 93.376, 93.009, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.5

Other elements in 2e0l:

The structure of Mutant Human Ribonuclease 1 (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 (Q28L, R31L, R32L) (pdb code 2e0l). 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 (Q28L, R31L, R32L), PDB code: 2e0l:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 2e0l

Go back to Cadmium Binding Sites List in 2e0l
Cadmium binding site 1 out of 8 in the Mutant Human Ribonuclease 1 (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 (Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:15.2
occ:0.50
 OE2 A:GLU125 2.3 29.1 1.0
OE1 A:GLU125 2.6 31.6 1.0
CD A:GLU125 2.8 31.2 1.0
NH2 A:ARG104 4.2 34.3 1.0
NH1 A:ARG104 4.2 30.8 1.0
CG A:GLU125 4.2 31.5 1.0
O A:HOH2089 4.5 36.5 1.0
CZ A:ARG104 4.6 32.2 1.0
CB A:GLU125 5.0 30.8 1.0

Cadmium binding site 2 out of 8 in 2e0l

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Cadmium binding site 2 out of 8 in the Mutant Human Ribonuclease 1 (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 (Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:18.5
occ:0.50
 CL A:CL2002 2.3 19.9 1.0
CL A:CL2001 2.5 29.0 1.0
O A:SER123 3.9 32.1 1.0
NE A:ARG104 4.4 30.1 1.0
O A:HOH2066 4.8 39.4 1.0
CA A:VAL124 4.9 31.9 1.0
C A:SER123 4.9 32.4 1.0
NH2 A:ARG104 5.0 34.3 1.0

Cadmium binding site 3 out of 8 in 2e0l

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Cadmium binding site 3 out of 8 in the Mutant Human Ribonuclease 1 (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 (Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:34.5
occ:1.00
 CL A:CL2005 2.5 35.9 1.0
CL A:CL2006 2.5 28.2 1.0
CB A:SER100 3.8 30.0 1.0
OG A:SER100 3.9 34.1 1.0
CD A:ARG85 4.2 35.6 1.0
O A:HOH2165 4.5 42.0 1.0
NE A:ARG85 4.6 44.6 1.0

Cadmium binding site 4 out of 8 in 2e0l

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Cadmium binding site 4 out of 8 in the Mutant Human Ribonuclease 1 (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 (Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1006

b:70.6
occ:1.00
 ND1 A:HIS119 2.3 36.1 1.0
O A:HOH2153 2.6 48.8 1.0
CL A:CL2009 2.7 43.3 1.0
CE1 A:HIS119 3.2 37.1 1.0
CG A:HIS119 3.4 35.5 1.0
O A:HOH2090 3.6 42.8 1.0
O A:HOH2188 3.7 55.8 1.0
CB A:HIS119 3.8 33.1 1.0
CA A:HIS119 4.1 32.6 1.0
O A:HOH2146 4.1 41.8 1.0
NE2 A:HIS119 4.3 36.4 1.0
O A:HOH2127 4.4 49.3 1.0
N A:PHE120 4.5 32.2 1.0
CD2 A:HIS119 4.5 35.8 1.0
O A:HOH2063 4.6 25.1 1.0
O A:PHE120 4.7 32.4 1.0
C A:HIS119 4.8 32.6 1.0
O A:VAL118 4.9 33.4 1.0

Cadmium binding site 5 out of 8 in 2e0l

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Cadmium binding site 5 out of 8 in the Mutant Human Ribonuclease 1 (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 (Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1008

b:36.7
occ:1.00
 ND1 A:HIS80 1.9 34.8 1.0
CL A:CL2011 2.3 34.0 1.0
O A:HOH2132 2.3 35.3 1.0
O A:HOH2122 2.5 40.3 1.0
OE1 A:GLU49 2.5 32.8 1.0
CE1 A:HIS80 2.5 30.8 1.0
O A:HOH2033 2.6 34.1 1.0
OE2 A:GLU49 3.0 32.6 1.0
CD A:GLU49 3.1 32.6 1.0
CG A:HIS80 3.2 30.2 1.0
NE2 A:HIS80 3.7 35.1 1.0
CB A:HIS80 3.8 28.5 1.0
O A:HIS48 4.0 30.5 1.0
CD2 A:HIS80 4.0 32.6 1.0
N A:HIS80 4.2 28.1 1.0
O A:HOH2019 4.2 20.9 1.0
O A:HOH2151 4.2 50.1 1.0
O A:HOH2158 4.3 47.1 1.0
O A:HOH2181 4.4 64.5 1.0
CG A:GLU49 4.5 31.9 1.0
O A:HOH2096 4.6 37.2 1.0
CA A:HIS80 4.7 29.0 1.0

Cadmium binding site 6 out of 8 in 2e0l

Go back to Cadmium Binding Sites List in 2e0l
Cadmium binding site 6 out of 8 in the Mutant Human Ribonuclease 1 (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 (Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1003

b:18.5
occ:0.50
 CL B:CL2004 2.8 20.3 1.0
CL B:CL2003 3.1 29.3 1.0
NE B:ARG104 4.1 31.1 1.0
O B:SER123 4.1 32.7 1.0
O B:HOH2126 4.1 34.5 1.0
NZ B:LYS102 4.3 40.5 1.0
NH2 B:ARG104 4.7 36.0 1.0
CD B:ARG104 4.8 31.7 1.0
CZ B:ARG104 4.9 33.8 1.0
OG B:SER123 4.9 38.6 1.0

Cadmium binding site 7 out of 8 in 2e0l

Go back to Cadmium Binding Sites List in 2e0l
Cadmium binding site 7 out of 8 in the Mutant Human Ribonuclease 1 (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 (Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1005

b:36.7
occ:1.00
 ND1 B:HIS80 2.0 34.4 1.0
CL B:CL2007 2.3 35.6 1.0
O B:HOH2093 2.4 37.0 1.0
O B:HOH2122 2.5 35.6 1.0
OE1 B:GLU49 2.5 32.7 1.0
CE1 B:HIS80 2.7 30.8 1.0
CL B:CL2008 2.7 48.1 1.0
OE2 B:GLU49 3.0 32.4 1.0
CD B:GLU49 3.1 33.2 1.0
CG B:HIS80 3.2 29.8 1.0
CB B:HIS80 3.8 27.9 1.0
NE2 B:HIS80 3.9 34.6 1.0
O B:HIS48 4.0 30.1 1.0
CD2 B:HIS80 4.2 32.4 1.0
N B:HIS80 4.2 28.4 1.0
O B:HOH2021 4.2 21.8 1.0
O B:HOH2172 4.3 57.1 1.0
CG B:GLU49 4.5 31.3 1.0
O B:HOH2097 4.7 36.4 1.0
CA B:HIS80 4.7 28.7 1.0

Cadmium binding site 8 out of 8 in 2e0l

Go back to Cadmium Binding Sites List in 2e0l
Cadmium binding site 8 out of 8 in the Mutant Human Ribonuclease 1 (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 (Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1007

b:73.4
occ:1.00
 ND1 B:HIS119 2.3 35.6 1.0
CL B:CL2010 2.8 43.0 1.0
O B:HOH2187 2.8 52.6 1.0
O B:HOH2205 3.1 54.3 1.0
CE1 B:HIS119 3.1 37.6 1.0
CG B:HIS119 3.4 36.3 1.0
CB B:HIS119 3.8 32.6 1.0
O B:HOH2109 3.9 47.2 1.0
CA B:HIS119 4.1 32.5 1.0
NE2 B:HIS119 4.3 37.0 1.0
O B:HOH2179 4.3 37.1 1.0
CD2 B:HIS119 4.5 35.2 1.0
N B:PHE120 4.5 32.4 1.0
O B:HOH2052 4.7 25.8 1.0
O B:PHE120 4.7 32.6 1.0
C B:HIS119 4.8 32.3 1.0
O B:VAL118 4.9 33.0 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 14:46:15 2024

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