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Manganese in PDB 5ze2: Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C

Enzymatic activity of Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C

All present enzymatic activity of Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C:
2.3.2.27;

Protein crystallography data

The structure of Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C, PDB code: 5ze2 was solved by M.S.Kim, W.Chuenchor, X.Chen, M.Gellert, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.63 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 132.770, 108.120, 155.740, 90.00, 114.45, 90.00
R / Rfree (%) 20 / 23.7

Other elements in 5ze2:

The structure of Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C also contains other interesting chemical elements:

Potassium (K) 2 atoms
Zinc (Zn) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C (pdb code 5ze2). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C, PDB code: 5ze2:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5ze2

Go back to Manganese Binding Sites List in 5ze2
Manganese binding site 1 out of 4 in the Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2002

b:92.6
occ:1.00
 O3' F:DG30 2.2 90.9 1.0
OD2 A:ASP600 2.2 83.0 1.0
OE1 A:GLU962 2.3 80.9 1.0
OE2 A:GLU962 2.7 70.7 1.0
CD A:GLU962 2.9 78.2 1.0
CG A:ASP600 3.2 86.8 1.0
C3' F:DG30 3.3 85.6 1.0
OD1 A:ASP600 3.4 88.6 1.0
MN A:MN2003 3.5 81.9 1.0
C4' F:DG30 3.6 68.7 1.0
O A:GLY601 4.1 79.5 1.0
OP1 F:DG30 4.2 69.0 1.0
C2' F:DG30 4.3 82.2 1.0
CG A:GLU962 4.4 74.0 1.0
C5' F:DG30 4.5 69.5 1.0
OD2 A:ASP708 4.5 89.3 1.0
CB A:ASP600 4.6 82.1 1.0
NE2 A:HIS795 4.6 85.5 1.0
ND2 A:ASN965 4.7 73.2 1.0
C1' F:DG30 4.7 79.1 1.0
CE1 A:HIS795 4.7 90.4 1.0
O4' F:DG30 4.7 76.0 1.0

Manganese binding site 2 out of 4 in 5ze2

Go back to Manganese Binding Sites List in 5ze2
Manganese binding site 2 out of 4 in the Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2003

b:81.9
occ:1.00
 OD2 A:ASP708 2.0 89.3 1.0
OD1 A:ASP600 2.4 88.6 1.0
CG A:ASP708 3.2 89.4 1.0
CG A:ASP600 3.4 86.8 1.0
MN A:MN2002 3.5 92.6 1.0
OE1 A:GLU662 3.6 90.6 1.0
OD1 A:ASP708 3.7 96.6 1.0
OD2 A:ASP600 3.8 83.0 1.0
O A:GLY601 4.2 79.5 1.0
CB A:ASP708 4.4 86.3 1.0
N A:GLY601 4.5 77.8 1.0
CD A:GLU662 4.6 95.1 1.0
OE1 A:GLU962 4.6 80.9 1.0
OE2 A:GLU662 4.7 95.3 1.0
O3' F:DG30 4.7 90.9 1.0
N6 I:DA16 4.8 0.6 0.8
CB A:ASP600 4.8 82.1 1.0

Manganese binding site 3 out of 4 in 5ze2

Go back to Manganese Binding Sites List in 5ze2
Manganese binding site 3 out of 4 in the Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2002

b:93.1
occ:1.00
 OD2 C:ASP708 2.0 91.1 1.0
OD1 C:ASP600 2.3 97.4 1.0
CG C:ASP708 3.1 91.2 1.0
CG C:ASP600 3.4 94.9 1.0
O4' J:DA16 3.6 1.0 0.8
MN C:MN2003 3.7 85.9 1.0
OD1 C:ASP708 3.8 0.0 1.0
OD2 C:ASP600 3.9 86.5 1.0
OE2 C:GLU662 3.9 0.4 1.0
OE1 C:GLU662 4.0 94.5 1.0
C1' J:DA16 4.0 0.6 0.8
O C:GLY601 4.0 82.2 1.0
CB C:ASP708 4.2 84.5 1.0
O3' G:DG41 4.2 86.1 1.0
C4' J:DA16 4.4 0.8 0.8
CD C:GLU662 4.4 0.2 1.0
OE1 C:GLU962 4.4 80.8 1.0
N C:GLY601 4.5 79.4 1.0
CB C:ASP600 4.7 89.7 1.0
N9 J:DA16 4.8 0.7 0.8
C8 J:DA16 4.8 0.1 0.8
C C:GLY601 5.0 81.4 1.0

Manganese binding site 4 out of 4 in 5ze2

Go back to Manganese Binding Sites List in 5ze2
Manganese binding site 4 out of 4 in the Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Hairpin Complex, RAG1/2-Hairpin 12RSS/23RSS Complex in 5MM MN2+ For 2 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2003

b:85.9
occ:1.00
 OE1 C:GLU962 2.0 80.8 1.0
O3' G:DG41 2.1 86.1 1.0
OE2 C:GLU962 2.2 90.5 1.0
CD C:GLU962 2.4 73.5 1.0
OD2 C:ASP600 2.5 86.5 1.0
CG C:ASP600 3.1 94.9 1.0
C3' G:DG41 3.2 81.8 1.0
OD1 C:ASP600 3.2 97.4 1.0
C4' G:DG41 3.6 75.4 1.0
MN C:MN2002 3.7 93.1 1.0
C2' G:DG41 3.7 77.0 1.0
CG C:GLU962 4.0 72.7 1.0
O C:GLY601 4.2 82.2 1.0
O5' G:DG41 4.3 81.2 1.0
C1' G:DG41 4.4 72.8 1.0
C5' G:DG41 4.4 74.7 1.0
CB C:ASP600 4.4 89.7 1.0
O4' G:DG41 4.7 72.1 1.0
NE2 C:HIS795 4.7 90.6 1.0
CE1 C:HIS795 4.8 82.9 1.0
CB C:GLU962 4.9 78.0 1.0
OD2 C:ASP708 4.9 91.1 1.0
OD1 C:ASN965 5.0 80.8 1.0

Reference:

M.S.Kim, W.Chuenchor, X.Chen, Y.Cui, X.Zhang, Z.H.Zhou, M.Gellert, W.Yang. Cracking the Dna Code For V(D)J Recombination Mol. Cell V. 70 358 2018.
ISSN: ISSN 1097-4164
PubMed: 29628308
DOI: 10.1016/J.MOLCEL.2018.03.008
Page generated: Sun Oct 6 03:39:17 2024

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