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Manganese in PDB 5ze1: Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C

Enzymatic activity of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C

All present enzymatic activity of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C:
2.3.2.27;

Protein crystallography data

The structure of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C, PDB code: 5ze1 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) 36.68 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 132.760, 108.600, 157.090, 90.00, 114.20, 90.00
R / Rfree (%) 19.7 / 23.2

Other elements in 5ze1:

The structure of Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 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 Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C (pdb code 5ze1). 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 Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C, PDB code: 5ze1:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5ze1

Go back to Manganese Binding Sites List in 5ze1
Manganese binding site 1 out of 4 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 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 Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2002

b:68.6
occ:1.00
 OD2 A:ASP600 2.0 57.0 1.0
OE1 A:GLU962 2.2 60.0 1.0
O3' F:DG30 2.2 75.2 1.0
OE2 A:GLU962 2.2 57.4 1.0
OP2 F:DT31 2.5 67.9 0.8
CD A:GLU962 2.6 57.7 1.0
CG A:ASP600 2.9 57.4 1.0
P F:DT31 2.9 70.5 0.8
OD1 A:ASP600 3.2 66.8 1.0
C3' F:DG30 3.5 59.2 1.0
MN A:MN2003 3.6 72.9 1.0
C4' F:DG30 3.8 50.1 1.0
O A:GLY601 3.8 57.3 1.0
ND2 A:ASN965 3.9 50.9 1.0
OP1 F:DT31 4.0 69.7 0.8
OP1 F:DG30 4.0 51.8 1.0
O5' F:DT31 4.1 81.8 0.8
CG A:GLU962 4.1 47.5 1.0
O A:HOH2104 4.1 74.7 1.0
C2' F:DG30 4.1 54.3 1.0
CB A:ASP600 4.3 57.9 1.0
O3' I:DA16 4.3 80.5 0.8
C5' F:DT31 4.4 84.3 0.8
C1' F:DG30 4.7 51.9 1.0
C5' F:DG30 4.7 52.9 1.0
O4' F:DG30 4.8 55.1 1.0
CE1 A:HIS795 5.0 59.3 1.0

Manganese binding site 2 out of 4 in 5ze1

Go back to Manganese Binding Sites List in 5ze1
Manganese binding site 2 out of 4 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 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 Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2003

b:72.9
occ:1.00
 OD2 A:ASP708 2.0 69.9 1.0
OD1 A:ASP600 2.2 66.8 1.0
O3' I:DA16 2.2 80.5 0.8
O A:HOH2104 2.2 74.7 1.0
OP2 F:DT31 2.2 67.9 0.8
O I:HOH101 2.8 84.9 1.0
CG A:ASP708 3.2 65.6 1.0
CG A:ASP600 3.3 57.4 1.0
C3' I:DA16 3.6 84.8 0.8
MN A:MN2002 3.6 68.6 1.0
P F:DT31 3.7 70.5 0.8
OD2 A:ASP600 3.8 57.0 1.0
OD1 A:ASP708 4.0 72.4 1.0
C4' I:DA16 4.1 80.4 0.8
OE1 A:GLU662 4.2 73.7 1.0
CB A:ASP708 4.2 59.0 1.0
N A:GLY601 4.4 58.5 1.0
O A:GLY601 4.4 57.3 1.0
OE2 A:GLU662 4.4 80.7 1.0
OE1 A:GLU962 4.4 60.0 1.0
C2' I:DA16 4.4 88.3 0.8
OP1 F:DT31 4.4 69.7 0.8
O3' F:DG30 4.6 75.2 1.0
CB A:ASP600 4.6 57.9 1.0
O5' F:DT31 4.6 81.8 0.8
CD A:GLU662 4.7 70.5 1.0
C5' F:DT31 4.7 84.3 0.8
C5' I:DA16 4.8 76.3 0.8
CA A:ASP600 4.8 60.2 1.0
NE2 A:HIS795 4.9 67.4 1.0

Manganese binding site 3 out of 4 in 5ze1

Go back to Manganese Binding Sites List in 5ze1
Manganese binding site 3 out of 4 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 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 Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2002

b:73.3
occ:1.00
 OD2 C:ASP708 1.9 71.2 1.0
O C:HOH2101 2.1 84.8 1.0
O C:HOH2106 2.3 63.4 1.0
O3' J:DA16 2.4 76.3 0.8
OD1 C:ASP600 2.4 68.6 1.0
OP2 G:DT42 2.7 68.7 0.8
CG C:ASP708 3.1 67.0 1.0
OD1 C:ASP708 3.6 67.0 1.0
CG C:ASP600 3.7 61.0 1.0
C3' J:DA16 3.7 82.3 0.8
OE1 C:GLU662 3.9 72.7 1.0
O5' G:DT42 3.9 76.0 0.8
P G:DT42 3.9 71.4 0.8
MN C:MN2003 4.0 65.2 1.0
OE2 C:GLU662 4.0 75.0 1.0
N C:GLY601 4.1 57.5 1.0
O C:GLY601 4.1 58.9 1.0
C4' J:DA16 4.3 82.7 0.8
CD C:GLU662 4.4 74.8 1.0
CB C:ASP708 4.5 53.8 1.0
OD2 C:ASP600 4.5 76.7 1.0
CB C:ASP600 4.6 53.9 1.0
C2' J:DA16 4.7 84.8 0.8
OE1 C:GLU962 4.7 58.0 1.0
CA C:ASP600 4.8 54.2 1.0
CA C:GLY601 4.8 57.8 1.0
C C:GLY601 4.9 55.0 1.0
OP1 G:DT42 4.9 69.1 0.8
C C:ASP600 4.9 55.7 1.0
O G:HOH103 5.0 58.3 1.0

Manganese binding site 4 out of 4 in 5ze1

Go back to Manganese Binding Sites List in 5ze1
Manganese binding site 4 out of 4 in the Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 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 Forming Complex, RAG1/2-Nicked 12RSS/23RSS Complex in 2MM MN2+ For 10 Min at 4'C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2003

b:65.2
occ:1.00
 OE1 C:GLU962 2.1 58.0 1.0
OE2 C:GLU962 2.1 55.4 1.0
OD2 C:ASP600 2.2 76.7 1.0
OP2 G:DT42 2.3 68.7 0.8
O G:HOH103 2.3 58.3 1.0
O3' G:DG41 2.4 63.9 1.0
CD C:GLU962 2.4 49.5 1.0
CG C:ASP600 2.7 61.0 1.0
OD1 C:ASP600 2.8 68.6 1.0
P G:DT42 2.9 71.4 0.8
O C:HOH2106 3.6 63.4 1.0
C3' G:DG41 3.6 49.1 1.0
O5' G:DT42 3.7 76.0 0.8
O C:GLY601 3.8 58.9 1.0
MN C:MN2002 4.0 73.3 1.0
CG C:GLU962 4.0 47.7 1.0
C2' G:DG41 4.1 44.8 1.0
OP1 G:DT42 4.2 69.1 0.8
C4' G:DG41 4.2 49.3 1.0
CB C:ASP600 4.2 53.9 1.0
OD1 C:ASN965 4.3 56.5 1.0
C5' G:DT42 4.5 80.4 0.8
OD2 C:ASP708 4.6 71.2 1.0
O5' G:DG41 4.7 58.9 1.0
O3' J:DA16 4.7 76.3 0.8
OP1 G:DG41 4.8 62.9 1.0
C C:GLY601 4.9 55.0 1.0
C1' G:DG41 4.9 46.6 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: Tue Dec 15 04:49:50 2020

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