Chlorine in PDB 8d58: Crystal Structure of Human METTL1-WDR4 Complex

Enzymatic activity of Crystal Structure of Human METTL1-WDR4 Complex

All present enzymatic activity of Crystal Structure of Human METTL1-WDR4 Complex:
2.1.1.33;

Protein crystallography data

The structure of Crystal Structure of Human METTL1-WDR4 Complex, PDB code: 8d58 was solved by R.Raj, K.Babu, Y.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.71 / 2.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.495, 91.113, 122.83, 90, 90, 90
R / Rfree (%) 20.3 / 22.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human METTL1-WDR4 Complex (pdb code 8d58). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Human METTL1-WDR4 Complex, PDB code: 8d58:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 8d58

Go back to Chlorine Binding Sites List in 8d58
Chlorine binding site 1 out of 6 in the Crystal Structure of Human METTL1-WDR4 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human METTL1-WDR4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:77.9
occ:1.00
 OG1 A:THR238 3.0 116.4 1.0
N A:GLY89 3.2 71.1 1.0
N A:TYR87 3.4 70.6 1.0
N A:GLU239 3.4 70.9 1.0
CA A:GLY89 3.7 58.2 1.0
CA A:THR238 3.7 72.2 1.0
N A:GLY88 3.8 68.9 1.0
C A:TYR87 3.8 67.6 1.0
CA A:TYR87 3.8 64.8 1.0
CB A:TYR87 3.8 62.9 1.0
CB A:THR238 4.0 59.3 1.0
C A:THR238 4.1 74.8 1.0
O A:CYS85 4.1 87.5 1.0
CB A:GLU239 4.1 87.7 1.0
CG A:GLU239 4.3 111.9 1.0
C A:GLY88 4.3 70.8 1.0
C A:GLY86 4.3 69.4 1.0
CA A:GLU239 4.4 81.3 1.0
O A:TYR87 4.5 75.0 1.0
CA A:GLY86 4.5 61.9 1.0
CA A:GLY88 4.6 65.6 1.0
CD2 A:TYR87 4.7 71.5 1.0
O A:SER237 4.8 76.6 1.0
CG A:TYR87 4.8 69.9 1.0
C A:GLY89 4.9 67.7 1.0
CD A:GLU239 5.0 126.3 1.0
N A:THR238 5.0 71.0 1.0
N A:LEU90 5.0 66.9 1.0

Chlorine binding site 2 out of 6 in 8d58

Go back to Chlorine Binding Sites List in 8d58
Chlorine binding site 2 out of 6 in the Crystal Structure of Human METTL1-WDR4 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human METTL1-WDR4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:88.4
occ:1.00
 O B:HOH503 3.2 59.0 1.0
OE2 A:GLU42 3.8 94.7 1.0
O B:PHE183 4.0 55.8 1.0
OE1 A:GLU42 4.1 83.6 1.0
CD A:PRO41 4.2 72.3 1.0
O A:HOH404 4.4 56.8 1.0
CD A:GLU42 4.4 87.7 1.0
CD1 B:LEU185 4.4 43.8 1.0
O B:GLY221 4.5 58.7 1.0
CE A:LYS40 4.6 88.4 1.0
CG A:PRO41 4.7 72.7 1.0
OH A:TYR186 4.8 68.7 1.0
O B:SER220 4.9 59.9 1.0
CG B:LEU185 5.0 50.7 1.0

Chlorine binding site 3 out of 6 in 8d58

Go back to Chlorine Binding Sites List in 8d58
Chlorine binding site 3 out of 6 in the Crystal Structure of Human METTL1-WDR4 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human METTL1-WDR4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:92.6
occ:1.00
 O B:CYS95 3.8 62.5 1.0
O B:HOH529 4.0 64.8 1.0
O B:LEU96 4.0 57.3 1.0
SG B:CYS95 4.1 71.8 1.0
CA B:SER97 4.3 62.0 1.0
C B:LEU96 4.4 53.0 1.0
N B:SER97 4.5 52.9 1.0
C B:CYS95 4.5 58.3 1.0
CB B:CYS95 4.6 44.0 1.0
CG2 B:VAL98 4.7 40.4 1.0
C B:SER97 4.8 52.8 1.0
N B:VAL98 4.8 57.7 1.0

Chlorine binding site 4 out of 6 in 8d58

Go back to Chlorine Binding Sites List in 8d58
Chlorine binding site 4 out of 6 in the Crystal Structure of Human METTL1-WDR4 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human METTL1-WDR4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:72.2
occ:1.00
 N B:PHE69 3.5 49.4 1.0
OG1 B:THR68 3.7 56.5 1.0
CB B:ALA8 4.0 46.5 1.0
CA B:THR68 4.0 48.4 1.0
CD2 B:PHE69 4.0 43.3 1.0
CB B:PHE69 4.1 49.0 1.0
C B:THR68 4.2 55.5 1.0
CA B:PHE69 4.4 42.3 1.0
CB B:THR68 4.4 48.9 1.0
CA B:ALA8 4.5 42.9 1.0
CG B:PHE69 4.6 46.5 1.0
N B:LEU9 4.6 69.2 1.0
O B:LEU9 4.9 63.8 1.0
O B:PHE69 4.9 43.4 1.0

Chlorine binding site 5 out of 6 in 8d58

Go back to Chlorine Binding Sites List in 8d58
Chlorine binding site 5 out of 6 in the Crystal Structure of Human METTL1-WDR4 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human METTL1-WDR4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:61.3
occ:1.00
 N B:ARG104 3.2 42.2 1.0
CG B:ARG104 3.4 47.8 1.0
NE B:ARG103 3.5 92.5 1.0
CE B:LYS83 3.5 75.1 1.0
NZ B:LYS83 3.8 66.3 1.0
CB B:ARG104 3.8 51.8 1.0
CB B:ARG103 3.8 52.2 1.0
CA B:ARG103 3.9 55.0 1.0
NH2 B:ARG103 3.9 69.9 1.0
C B:ARG103 4.0 62.9 1.0
CA B:ARG104 4.1 52.0 1.0
NE B:ARG104 4.1 79.2 1.0
CG B:ARG103 4.1 76.2 1.0
CZ B:ARG103 4.2 80.8 1.0
CD B:ARG104 4.4 50.8 1.0
CD B:ARG103 4.4 94.9 1.0
CZ B:ARG104 4.5 86.9 1.0
CD B:LYS83 4.6 54.8 1.0
NH2 B:ARG104 4.8 104.6 1.0
NH1 B:ARG104 4.9 80.9 1.0
CG B:LYS83 5.0 49.7 1.0

Chlorine binding site 6 out of 6 in 8d58

Go back to Chlorine Binding Sites List in 8d58
Chlorine binding site 6 out of 6 in the Crystal Structure of Human METTL1-WDR4 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human METTL1-WDR4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:89.2
occ:1.00
 OG B:SER128 3.2 56.9 1.0
O B:HOH502 3.8 60.3 1.0
O B:SER128 3.8 52.4 1.0
CE B:LYS116 3.9 54.8 1.0
NZ B:LYS116 3.9 87.4 1.0
CB B:SER128 4.2 43.5 1.0
CB B:ARG139 4.3 50.8 1.0
C B:SER128 4.3 50.8 1.0
CD B:LYS116 4.3 65.5 1.0
NE B:ARG139 4.3 82.3 1.0
CZ B:ARG139 4.3 82.4 1.0
NH2 B:ARG139 4.4 87.0 1.0
N B:SER130 4.5 51.9 1.0
N B:PHE129 4.7 48.0 1.0
C B:PHE129 4.9 48.8 1.0
CA B:PHE129 4.9 38.0 1.0
CD B:ARG139 4.9 77.0 1.0
CA B:SER128 4.9 38.0 1.0
NH1 B:ARG139 4.9 94.3 1.0
CG B:LYS116 4.9 49.7 1.0
N B:ARG139 4.9 50.3 1.0
O B:CYS137 5.0 56.3 1.0
OE2 B:GLU141 5.0 58.1 1.0

Reference:

V.M.Ruiz-Arroyo, R.Raj, K.Babu, O.Onolbaatar, P.H.Roberts, Y.Nam. Structures and Mechanisms of Trna Methylation By METTL1-WDR4. Nature 2023.
ISSN: ESSN 1476-4687
PubMed: 36599982
DOI: 10.1038/S41586-022-05565-5
Page generated: Tue Jul 30 08:25:42 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy