Atomistry » Cadmium » PDB 1ykq-2eik » 2e0l
Atomistry »
  Cadmium »
    PDB 1ykq-2eik »
      2e0l »

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

Go back to Cadmium Binding Sites List in 2e0l
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

Go back to Cadmium Binding Sites List in 2e0l
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

Go back to Cadmium Binding Sites List in 2e0l
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

Go back to Cadmium Binding Sites List in 2e0l
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy