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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

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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

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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

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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: Sun Jul 13 10:32:53 2025

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