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Chlorine 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:

Cadmium (Cd) 8 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L), PDB code: 2e0m:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 2e0m

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Chlorine binding site 1 out of 11 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl2001

b:27.9
occ:1.00
 CD A:CD1002 2.4 18.4 0.5
O A:HOH2090 3.5 26.0 1.0
CL A:CL2002 3.5 20.6 1.0

Chlorine binding site 2 out of 11 in 2e0m

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Chlorine binding site 2 out of 11 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl2002

b:20.6
occ:1.00
 CD A:CD1002 2.4 18.4 0.5
N A:GLU125 3.2 33.9 1.0
CL A:CL2001 3.5 27.9 1.0
O A:HOH2090 3.5 26.0 1.0
NE A:ARG104 3.7 33.0 1.0
CB A:GLU125 3.8 35.0 1.0
CA A:VAL124 3.8 34.3 1.0
C A:VAL124 4.0 34.2 1.0
O A:HOH2109 4.0 29.0 1.0
CA A:GLU125 4.1 34.6 1.0
CD A:ARG104 4.2 33.3 1.0
CZ A:ARG104 4.2 34.2 1.0
NH2 A:ARG104 4.3 34.4 1.0
O A:SER123 4.5 32.9 1.0
CB A:VAL124 4.7 35.8 1.0
N A:VAL124 4.8 34.5 1.0
OE2 A:GLU125 4.8 30.8 1.0

Chlorine binding site 3 out of 11 in 2e0m

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Chlorine binding site 3 out of 11 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl2003

b:27.8
occ:1.00
 CD B:CD1003 2.8 18.2 0.5
O B:HOH2032 3.6 26.3 1.0
CL B:CL2004 3.6 21.3 1.0

Chlorine binding site 4 out of 11 in 2e0m

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Chlorine binding site 4 out of 11 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2004

b:21.3
occ:1.00
 CD B:CD1003 2.8 18.2 0.5
N B:GLU125 3.2 33.5 1.0
CL B:CL2003 3.6 27.8 1.0
NE B:ARG104 3.6 33.9 1.0
CB B:GLU125 3.8 35.1 1.0
CA B:VAL124 3.8 34.2 1.0
C B:VAL124 3.9 34.4 1.0
O B:HOH2140 4.0 29.0 1.0
CA B:GLU125 4.1 34.6 1.0
CD B:ARG104 4.2 32.9 1.0
CZ B:ARG104 4.2 33.3 1.0
NH2 B:ARG104 4.3 34.7 1.0
O B:SER123 4.5 33.2 1.0
CB B:VAL124 4.6 35.9 1.0
N B:VAL124 4.8 34.6 1.0
OE2 B:GLU125 4.9 31.8 1.0
O B:HOH2032 5.0 26.3 1.0

Chlorine binding site 5 out of 11 in 2e0m

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Chlorine binding site 5 out of 11 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2005

b:45.2
occ:1.00
 CD A:CD1004 2.7 49.5 1.0
OD2 A:ASP83 3.3 43.5 1.0
NZ A:LYS102 3.5 40.9 1.0
CB A:ASP83 3.6 35.4 1.0
O A:HOH2111 3.7 30.4 1.0
CB A:SER100 3.7 33.2 1.0
OG A:SER100 3.8 38.7 1.0
CD A:ARG85 3.8 37.7 1.0
CG A:ASP83 3.9 40.4 1.0
NE A:ARG85 4.0 47.8 1.0
CL A:CL2006 4.2 31.8 1.0
CE A:LYS102 4.4 41.4 1.0
CG A:ARG85 4.5 36.3 1.0
O A:HOH2108 4.9 40.4 1.0
O A:HOH2116 4.9 43.9 1.0
CA A:ASP83 5.0 34.4 1.0

Chlorine binding site 6 out of 11 in 2e0m

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Chlorine binding site 6 out of 11 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl2006

b:31.8
occ:1.00
 CD A:CD1004 2.6 49.5 1.0
O A:HOH2201 2.7 43.6 1.0
O A:HOH2108 3.0 40.4 1.0
O A:HOH2073 3.6 42.9 1.0
O A:HOH2084 3.7 37.3 1.0
CD A:ARG85 3.7 37.7 1.0
CL A:CL2005 4.2 45.2 1.0
NE A:ARG85 4.4 47.8 1.0
O A:HOH2111 4.7 30.4 1.0
CG A:ARG85 5.0 36.3 1.0

Chlorine binding site 7 out of 11 in 2e0m

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Chlorine binding site 7 out of 11 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl2007

b:35.2
occ:1.00
 CD B:CD1005 2.3 34.9 1.0
O B:HOH2021 2.6 20.3 1.0
O B:HOH2108 2.8 38.4 1.0
OE1 B:GLU49 3.0 34.8 1.0
CL B:CL2008 3.3 57.7 1.0
ND1 B:HIS80 3.4 35.5 1.0
CE1 B:HIS80 3.7 32.6 1.0
O B:SER78 3.8 37.6 1.0
CD B:GLU49 3.8 34.9 1.0
OE2 B:GLU49 3.8 34.8 1.0
O B:HOH2037 3.9 26.2 1.0
O B:HOH2124 4.2 46.8 1.0
O B:HOH2098 4.2 37.3 1.0
N B:HIS80 4.3 30.5 1.0
CA B:MET79 4.4 33.9 1.0
CG B:HIS80 4.5 32.5 1.0
O B:HOH2061 4.7 36.2 1.0
O B:HOH2129 4.8 35.6 1.0
C B:MET79 4.8 34.5 1.0
NE2 B:HIS80 4.8 36.4 1.0
O B:HOH2128 4.8 40.5 1.0
C B:SER78 4.8 36.1 1.0

Chlorine binding site 8 out of 11 in 2e0m

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Chlorine binding site 8 out of 11 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2008

b:57.7
occ:1.00
 CD B:CD1005 2.6 34.9 1.0
CL B:CL2007 3.3 35.2 1.0
CE1 B:HIS80 3.4 32.6 1.0
ND1 B:HIS80 3.7 35.5 1.0
O B:HOH2124 3.8 46.8 1.0
O B:HOH2129 3.9 35.6 1.0
O B:HOH2145 4.6 59.9 1.0
O B:HOH2131 4.6 50.3 1.0
NE2 B:HIS80 4.7 36.4 1.0
OE2 B:GLU49 4.7 34.8 1.0
OE1 B:GLU49 4.9 34.8 1.0
O B:HOH2021 4.9 20.3 1.0

Chlorine binding site 9 out of 11 in 2e0m

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Chlorine binding site 9 out of 11 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2009

b:44.6
occ:1.00
 CD A:CD1006 2.7 91.9 1.0
O A:HOH2087 2.7 25.2 1.0
N A:PHE120 2.9 34.8 1.0
NE2 A:HIS12 3.0 34.9 1.0
O A:HOH2074 3.2 45.0 1.0
O A:HOH2128 3.4 44.1 1.0
CA A:HIS119 3.4 36.1 1.0
CD2 A:HIS12 3.6 34.6 1.0
C A:HIS119 3.7 35.5 1.0
ND1 A:HIS119 3.7 43.3 1.0
CA A:PHE120 3.9 34.8 1.0
CB A:PHE120 4.0 34.7 1.0
CE1 A:HIS12 4.1 37.0 1.0
O A:PHE120 4.1 35.4 1.0
CB A:HIS119 4.2 37.1 1.0
OE1 A:GLN11 4.2 36.4 1.0
CG A:HIS119 4.2 40.3 1.0
O A:VAL118 4.4 35.7 1.0
C A:PHE120 4.5 34.5 1.0
N A:HIS119 4.5 35.6 1.0
O A:HOH2157 4.5 67.5 1.0
CE1 A:HIS119 4.6 42.8 1.0
CD1 A:PHE8 4.7 33.0 1.0
CG A:HIS12 4.8 35.2 1.0
C A:VAL118 4.9 35.0 1.0
O A:HIS119 4.9 35.2 1.0
O A:HOH2032 4.9 30.7 1.0

Chlorine binding site 10 out of 11 in 2e0m

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Chlorine binding site 10 out of 11 in the Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Mutant Human Ribonuclease 1 (T24L, Q28L, R31L, R32L) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2010

b:47.1
occ:1.00
 O B:HOH2043 2.7 26.5 1.0
CD B:CD1007 2.7 88.6 1.0
O B:HOH2141 2.9 48.5 1.0
NE2 B:HIS12 3.0 34.8 1.0
N B:PHE120 3.0 35.0 1.0
O B:HOH2093 3.1 41.2 1.0
O B:HOH2135 3.5 50.9 1.0
CA B:HIS119 3.5 36.1 1.0
CD2 B:HIS12 3.6 34.5 1.0
C B:HIS119 3.7 35.5 1.0
ND1 B:HIS119 3.8 42.0 1.0
CA B:PHE120 4.0 35.1 1.0
CE1 B:HIS12 4.0 37.0 1.0
O B:HOH2160 4.0 60.6 1.0
CB B:PHE120 4.0 34.9 1.0
NE2 B:GLN11 4.1 33.7 1.0
O B:HOH2195 4.2 48.7 1.0
O B:PHE120 4.2 35.5 1.0
CB B:HIS119 4.3 36.8 1.0
CG B:HIS119 4.3 39.7 1.0
O B:VAL118 4.5 35.7 1.0
C B:PHE120 4.5 34.7 1.0
N B:HIS119 4.6 35.7 1.0
CE1 B:HIS119 4.7 42.3 1.0
CG B:HIS12 4.8 35.3 1.0
CD1 B:PHE8 4.8 34.1 1.0
O B:HOH2033 4.9 27.9 1.0
O B:HIS119 5.0 35.4 1.0
C B:VAL118 5.0 35.0 1.0
ND1 B:HIS12 5.0 35.3 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: Sat Jul 20 06:43:00 2024

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